From d59ecf72d0fbd22bfe2c8d924b637ae6124bbb00 Mon Sep 17 00:00:00 2001 From: Pablo Date: Thu, 16 May 2024 17:09:32 +0200 Subject: [PATCH 01/40] appy changes for ARM Signed-off-by: Pablo --- modules/local/star_align_igenomes/main.nf | 2 +- modules/local/star_genomegenerate_igenomes/main.nf | 2 +- modules/nf-core/bbmap/bbsplit/environment.yml | 2 +- modules/nf-core/bedtools/genomecov/environment.yml | 3 ++- modules/nf-core/bedtools/genomecov/main.nf | 2 +- modules/nf-core/cat/fastq/environment.yml | 2 +- modules/nf-core/custom/catadditionalfasta/environment.yml | 2 +- modules/nf-core/custom/getchromsizes/environment.yml | 2 +- modules/nf-core/custom/tx2gene/environment.yml | 2 +- modules/nf-core/dupradar/environment.yml | 2 +- modules/nf-core/fastp/environment.yml | 2 +- modules/nf-core/fastqc/environment.yml | 2 +- modules/nf-core/fq/subsample/environment.yml | 2 +- modules/nf-core/gffread/environment.yml | 2 +- modules/nf-core/gunzip/environment.yml | 2 +- modules/nf-core/hisat2/align/environment.yml | 4 ++-- modules/nf-core/hisat2/build/environment.yml | 2 +- modules/nf-core/hisat2/extractsplicesites/environment.yml | 2 +- modules/nf-core/kallisto/index/environment.yml | 2 +- modules/nf-core/kallisto/quant/environment.yml | 2 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/picard/markduplicates/environment.yml | 2 +- modules/nf-core/preseq/lcextrap/environment.yml | 2 +- modules/nf-core/qualimap/rnaseq/environment.yml | 2 +- modules/nf-core/rsem/calculateexpression/environment.yml | 5 +++-- modules/nf-core/rsem/preparereference/environment.yml | 5 +++-- modules/nf-core/rseqc/bamstat/environment.yml | 4 ++-- modules/nf-core/rseqc/inferexperiment/environment.yml | 4 ++-- modules/nf-core/rseqc/innerdistance/environment.yml | 4 ++-- modules/nf-core/rseqc/junctionannotation/environment.yml | 4 ++-- modules/nf-core/rseqc/junctionsaturation/environment.yml | 4 ++-- modules/nf-core/rseqc/readdistribution/environment.yml | 4 ++-- modules/nf-core/rseqc/readduplication/environment.yml | 4 ++-- modules/nf-core/rseqc/tin/environment.yml | 4 ++-- modules/nf-core/salmon/index/environment.yml | 2 +- modules/nf-core/salmon/quant/environment.yml | 2 +- modules/nf-core/samtools/flagstat/environment.yml | 4 ++-- modules/nf-core/samtools/idxstats/environment.yml | 4 ++-- modules/nf-core/samtools/index/environment.yml | 4 ++-- modules/nf-core/samtools/sort/environment.yml | 4 ++-- modules/nf-core/samtools/sort/main.nf | 1 - modules/nf-core/samtools/stats/environment.yml | 4 ++-- modules/nf-core/sortmerna/environment.yml | 2 +- modules/nf-core/star/align/environment.yml | 8 ++++---- modules/nf-core/star/genomegenerate/environment.yml | 8 ++++---- modules/nf-core/stringtie/stringtie/environment.yml | 2 +- modules/nf-core/subread/featurecounts/environment.yml | 2 +- .../summarizedexperiment/environment.yml | 2 +- modules/nf-core/trimgalore/environment.yml | 4 ++-- modules/nf-core/tximeta/tximport/environment.yml | 2 +- modules/nf-core/ucsc/bedclip/environment.yml | 2 +- modules/nf-core/ucsc/bedgraphtobigwig/environment.yml | 2 +- modules/nf-core/umitools/dedup/environment.yml | 2 +- modules/nf-core/umitools/extract/environment.yml | 2 +- modules/nf-core/umitools/prepareforrsem/environment.yml | 2 +- modules/nf-core/untar/environment.yml | 6 +++--- nextflow.config | 2 +- workflows/rnaseq/main.nf | 2 +- 58 files changed, 85 insertions(+), 83 deletions(-) diff --git a/modules/local/star_align_igenomes/main.nf b/modules/local/star_align_igenomes/main.nf index 32f3cac29..22981ed06 100644 --- a/modules/local/star_align_igenomes/main.nf +++ b/modules/local/star_align_igenomes/main.nf @@ -2,7 +2,7 @@ process STAR_ALIGN_IGENOMES { tag "$meta.id" label 'process_high' - conda "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0" + conda "seqera::star=2.6.1d bioconda::samtools conda-forge::gawk=5.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' : 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }" diff --git a/modules/local/star_genomegenerate_igenomes/main.nf b/modules/local/star_genomegenerate_igenomes/main.nf index 814bc7c8c..c36025b05 100644 --- a/modules/local/star_genomegenerate_igenomes/main.nf +++ b/modules/local/star_genomegenerate_igenomes/main.nf @@ -2,7 +2,7 @@ process STAR_GENOMEGENERATE_IGENOMES { tag "$fasta" label 'process_high' - conda "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0" + conda "bioconda::star bioconda::samtools conda-forge::gawk=5.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' : 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }" diff --git a/modules/nf-core/bbmap/bbsplit/environment.yml b/modules/nf-core/bbmap/bbsplit/environment.yml index 4c6db6276..2e7bb8194 100644 --- a/modules/nf-core/bbmap/bbsplit/environment.yml +++ b/modules/nf-core/bbmap/bbsplit/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::bbmap=39.01 + - bioconda::bbmap diff --git a/modules/nf-core/bedtools/genomecov/environment.yml b/modules/nf-core/bedtools/genomecov/environment.yml index 8fbe20c31..4d4e55eaf 100644 --- a/modules/nf-core/bedtools/genomecov/environment.yml +++ b/modules/nf-core/bedtools/genomecov/environment.yml @@ -1,7 +1,8 @@ name: bedtools_genomecov channels: + - seqera - conda-forge - bioconda - defaults dependencies: - - bioconda::bedtools=2.31.1 + - bioconda::bedtools diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 954e8913d..b02bf1cfe 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -27,7 +27,7 @@ process BEDTOOLS_GENOMECOV { if (!args_list.contains('-bg') && (scale > 0 && scale != 1)) { args += " -bg" } - def sort_cmd = sort ? '| bedtools sort' : '' + def sort_cmd = sort ? '| sort -k1,1 -k2,2n' : '' def prefix = task.ext.prefix ?: "${meta.id}" if (intervals.name =~ /\.bam/) { diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index 8c69b121f..7a9bebebf 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - conda-forge::coreutils=8.30 + - conda-forge::coreutils diff --git a/modules/nf-core/custom/catadditionalfasta/environment.yml b/modules/nf-core/custom/catadditionalfasta/environment.yml index 5e757bf4c..a801ae936 100644 --- a/modules/nf-core/custom/catadditionalfasta/environment.yml +++ b/modules/nf-core/custom/catadditionalfasta/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - conda-forge::python=3.9.5" + - conda-forge::python" diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml index 2a01695f1..7555c59ee 100644 --- a/modules/nf-core/custom/getchromsizes/environment.yml +++ b/modules/nf-core/custom/getchromsizes/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.16.1 + - bioconda::samtools diff --git a/modules/nf-core/custom/tx2gene/environment.yml b/modules/nf-core/custom/tx2gene/environment.yml index a859dc881..638bc4a75 100644 --- a/modules/nf-core/custom/tx2gene/environment.yml +++ b/modules/nf-core/custom/tx2gene/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - python=3.9.5 + - python diff --git a/modules/nf-core/dupradar/environment.yml b/modules/nf-core/dupradar/environment.yml index 58b2bf11d..0f6aa3d2b 100644 --- a/modules/nf-core/dupradar/environment.yml +++ b/modules/nf-core/dupradar/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::bioconductor-dupradar=1.32.0" + - "bioconda::bioconductor-dupradar" diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml index 70389e664..6970ba186 100644 --- a/modules/nf-core/fastp/environment.yml +++ b/modules/nf-core/fastp/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::fastp=0.23.4 + - bioconda::fastp diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 1787b38a9..936bf0896 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::fastqc=0.12.1 + - bioconda::fastqc diff --git a/modules/nf-core/fq/subsample/environment.yml b/modules/nf-core/fq/subsample/environment.yml index c588de38a..71231aa8b 100644 --- a/modules/nf-core/fq/subsample/environment.yml +++ b/modules/nf-core/fq/subsample/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::fq=0.9.1 + - bioconda::fq diff --git a/modules/nf-core/gffread/environment.yml b/modules/nf-core/gffread/environment.yml index 5398f71c5..17e6bb6cb 100644 --- a/modules/nf-core/gffread/environment.yml +++ b/modules/nf-core/gffread/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gffread=0.12.1 + - bioconda::gffread diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml index 25910b340..d05be27a8 100644 --- a/modules/nf-core/gunzip/environment.yml +++ b/modules/nf-core/gunzip/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - conda-forge::sed=4.7 + - conda-forge::sed diff --git a/modules/nf-core/hisat2/align/environment.yml b/modules/nf-core/hisat2/align/environment.yml index 0c1415f94..f10c74a40 100644 --- a/modules/nf-core/hisat2/align/environment.yml +++ b/modules/nf-core/hisat2/align/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::hisat2=2.2.1 - - bioconda::samtools=1.16.1 + - bioconda::hisat2 + - bioconda::samtools diff --git a/modules/nf-core/hisat2/build/environment.yml b/modules/nf-core/hisat2/build/environment.yml index 2e67cd3ea..78fa8b257 100644 --- a/modules/nf-core/hisat2/build/environment.yml +++ b/modules/nf-core/hisat2/build/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::hisat2=2.2.1 + - bioconda::hisat2 diff --git a/modules/nf-core/hisat2/extractsplicesites/environment.yml b/modules/nf-core/hisat2/extractsplicesites/environment.yml index 4b03e5e46..4ae5a0986 100644 --- a/modules/nf-core/hisat2/extractsplicesites/environment.yml +++ b/modules/nf-core/hisat2/extractsplicesites/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::hisat2=2.2.1 + - bioconda::hisat2 diff --git a/modules/nf-core/kallisto/index/environment.yml b/modules/nf-core/kallisto/index/environment.yml index 471b006a8..5ddd1ce3f 100644 --- a/modules/nf-core/kallisto/index/environment.yml +++ b/modules/nf-core/kallisto/index/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::kallisto=0.48.0 + - bioconda::kallisto diff --git a/modules/nf-core/kallisto/quant/environment.yml b/modules/nf-core/kallisto/quant/environment.yml index c2d6306bb..8b95f28f3 100644 --- a/modules/nf-core/kallisto/quant/environment.yml +++ b/modules/nf-core/kallisto/quant/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::kallisto=0.48.0 + - bioconda::kallisto diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index ca39fb67e..7c7e1e5d7 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.21 + - bioconda::multiqc diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml index 58b795f54..7e0b0b34c 100644 --- a/modules/nf-core/picard/markduplicates/environment.yml +++ b/modules/nf-core/picard/markduplicates/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard diff --git a/modules/nf-core/preseq/lcextrap/environment.yml b/modules/nf-core/preseq/lcextrap/environment.yml index 57b8b9c67..7d8613bcc 100644 --- a/modules/nf-core/preseq/lcextrap/environment.yml +++ b/modules/nf-core/preseq/lcextrap/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::preseq=3.1.2 + - bioconda::preseq diff --git a/modules/nf-core/qualimap/rnaseq/environment.yml b/modules/nf-core/qualimap/rnaseq/environment.yml index 590ae85f7..f1f0b04db 100644 --- a/modules/nf-core/qualimap/rnaseq/environment.yml +++ b/modules/nf-core/qualimap/rnaseq/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::qualimap=2.3 + - bioconda::qualimap diff --git a/modules/nf-core/rsem/calculateexpression/environment.yml b/modules/nf-core/rsem/calculateexpression/environment.yml index b811fa6fe..47d0158ab 100644 --- a/modules/nf-core/rsem/calculateexpression/environment.yml +++ b/modules/nf-core/rsem/calculateexpression/environment.yml @@ -1,8 +1,9 @@ name: rsem_calculateexpression channels: + - seqera - conda-forge - bioconda - defaults dependencies: - - bioconda::rsem=1.3.3 - - bioconda::star=2.7.10a + - bioconda::rsem + - bioconda::star diff --git a/modules/nf-core/rsem/preparereference/environment.yml b/modules/nf-core/rsem/preparereference/environment.yml index c80e69106..c4ef537cb 100644 --- a/modules/nf-core/rsem/preparereference/environment.yml +++ b/modules/nf-core/rsem/preparereference/environment.yml @@ -1,8 +1,9 @@ name: rsem_preparereference channels: + - seqera - conda-forge - bioconda - defaults dependencies: - - bioconda::rsem=1.3.3 - - bioconda::star=2.7.10a + - seqera::rsem + - seqera::star=2.6.1d diff --git a/modules/nf-core/rseqc/bamstat/environment.yml b/modules/nf-core/rseqc/bamstat/environment.yml index e960c9943..2894094ee 100644 --- a/modules/nf-core/rseqc/bamstat/environment.yml +++ b/modules/nf-core/rseqc/bamstat/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/inferexperiment/environment.yml b/modules/nf-core/rseqc/inferexperiment/environment.yml index 78215985a..e6affc939 100644 --- a/modules/nf-core/rseqc/inferexperiment/environment.yml +++ b/modules/nf-core/rseqc/inferexperiment/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/innerdistance/environment.yml b/modules/nf-core/rseqc/innerdistance/environment.yml index fb6e9e925..bb7838a3f 100644 --- a/modules/nf-core/rseqc/innerdistance/environment.yml +++ b/modules/nf-core/rseqc/innerdistance/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/junctionannotation/environment.yml b/modules/nf-core/rseqc/junctionannotation/environment.yml index 35276b715..9c43c0d5a 100644 --- a/modules/nf-core/rseqc/junctionannotation/environment.yml +++ b/modules/nf-core/rseqc/junctionannotation/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/junctionsaturation/environment.yml b/modules/nf-core/rseqc/junctionsaturation/environment.yml index 7b9cc4fa7..7e2607545 100644 --- a/modules/nf-core/rseqc/junctionsaturation/environment.yml +++ b/modules/nf-core/rseqc/junctionsaturation/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/readdistribution/environment.yml b/modules/nf-core/rseqc/readdistribution/environment.yml index 59be9fa88..dcdc0defd 100644 --- a/modules/nf-core/rseqc/readdistribution/environment.yml +++ b/modules/nf-core/rseqc/readdistribution/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/readduplication/environment.yml b/modules/nf-core/rseqc/readduplication/environment.yml index c99f107a1..3600c7054 100644 --- a/modules/nf-core/rseqc/readduplication/environment.yml +++ b/modules/nf-core/rseqc/readduplication/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/tin/environment.yml b/modules/nf-core/rseqc/tin/environment.yml index 288da4300..f24194b5f 100644 --- a/modules/nf-core/rseqc/tin/environment.yml +++ b/modules/nf-core/rseqc/tin/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/salmon/index/environment.yml b/modules/nf-core/salmon/index/environment.yml index a6607d964..29f762517 100644 --- a/modules/nf-core/salmon/index/environment.yml +++ b/modules/nf-core/salmon/index/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::salmon=1.10.1 + - bioconda::salmon diff --git a/modules/nf-core/salmon/quant/environment.yml b/modules/nf-core/salmon/quant/environment.yml index 862667241..28439bdbe 100644 --- a/modules/nf-core/salmon/quant/environment.yml +++ b/modules/nf-core/salmon/quant/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::salmon=1.10.1 + - bioconda::salmon diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index bd57cb54d..cd58f431d 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools + - bioconda::htslib diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index 174973b88..5d0378237 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools + - bioconda::htslib diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index a5e506498..84b752bde 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools + - bioconda::htslib diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index 4d898e486..fbb6233ea 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools + - bioconda::htslib diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index fc374f980..0aed6b796 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -32,7 +32,6 @@ process SAMTOOLS_SORT { """ samtools cat \\ - --threads $task.cpus \\ ${bam} \\ | \\ samtools sort \\ diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index 67bb0ca40..74f55132b 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools + - bioconda::htslib diff --git a/modules/nf-core/sortmerna/environment.yml b/modules/nf-core/sortmerna/environment.yml index f40f9958d..369a72994 100644 --- a/modules/nf-core/sortmerna/environment.yml +++ b/modules/nf-core/sortmerna/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::sortmerna=4.3.6 + - bioconda::sortmerna diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml index 8bd58cff5..f639ccfb0 100644 --- a/modules/nf-core/star/align/environment.yml +++ b/modules/nf-core/star/align/environment.yml @@ -4,7 +4,7 @@ channels: - bioconda - defaults dependencies: - - bioconda::star=2.7.10a - - bioconda::samtools=1.18 - - bioconda::htslib=1.18 - - conda-forge::gawk=5.1.0 + - bioconda::star + - bioconda::samtools + - bioconda::htslib + - conda-forge::gawk diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml index 791f255e5..1170105b5 100644 --- a/modules/nf-core/star/genomegenerate/environment.yml +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -4,7 +4,7 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.18 - - bioconda::htslib=1.18 - - bioconda::star=2.7.10a - - conda-forge::gawk=5.1.0 + - bioconda::samtools + - bioconda::htslib + - bioconda::star + - conda-forge::gawk diff --git a/modules/nf-core/stringtie/stringtie/environment.yml b/modules/nf-core/stringtie/stringtie/environment.yml index 7a0eccdb8..7c3a0158d 100644 --- a/modules/nf-core/stringtie/stringtie/environment.yml +++ b/modules/nf-core/stringtie/stringtie/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::stringtie=2.2.1 + - bioconda::stringtie diff --git a/modules/nf-core/subread/featurecounts/environment.yml b/modules/nf-core/subread/featurecounts/environment.yml index ca19439d7..812744486 100644 --- a/modules/nf-core/subread/featurecounts/environment.yml +++ b/modules/nf-core/subread/featurecounts/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::subread=2.0.1 + - bioconda::subread diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml index 252ace791..f97e7d943 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::bioconductor-summarizedexperiment=1.32.0" + - "bioconda::bioconductor-summarizedexperiment" diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml index 17b39f4a5..234bca959 100644 --- a/modules/nf-core/trimgalore/environment.yml +++ b/modules/nf-core/trimgalore/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::trim-galore=0.6.7 - - bioconda::cutadapt=3.4 + - bioconda::trim-galore + - bioconda::cutadapt diff --git a/modules/nf-core/tximeta/tximport/environment.yml b/modules/nf-core/tximeta/tximport/environment.yml index 24b202222..4649d1759 100644 --- a/modules/nf-core/tximeta/tximport/environment.yml +++ b/modules/nf-core/tximeta/tximport/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::bioconductor-tximeta=1.20.1" + - "bioconda::bioconductor-tximeta" diff --git a/modules/nf-core/ucsc/bedclip/environment.yml b/modules/nf-core/ucsc/bedclip/environment.yml index 571dc2749..ae7bcb0d1 100644 --- a/modules/nf-core/ucsc/bedclip/environment.yml +++ b/modules/nf-core/ucsc/bedclip/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::ucsc-bedclip=377 + - bioconda::ucsc-bedclip diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml index f91e216f5..1e6658778 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml +++ b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::ucsc-bedgraphtobigwig=445 + - bioconda::ucsc-bedgraphtobigwig diff --git a/modules/nf-core/umitools/dedup/environment.yml b/modules/nf-core/umitools/dedup/environment.yml index bc497824f..173040160 100644 --- a/modules/nf-core/umitools/dedup/environment.yml +++ b/modules/nf-core/umitools/dedup/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::umi_tools=1.1.5 + - bioconda::umi_tools diff --git a/modules/nf-core/umitools/extract/environment.yml b/modules/nf-core/umitools/extract/environment.yml index aab452d1e..0d979b32c 100644 --- a/modules/nf-core/umitools/extract/environment.yml +++ b/modules/nf-core/umitools/extract/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::umi_tools=1.1.5 + - bioconda::umi_tools diff --git a/modules/nf-core/umitools/prepareforrsem/environment.yml b/modules/nf-core/umitools/prepareforrsem/environment.yml index dbb1bde77..cf83ff218 100644 --- a/modules/nf-core/umitools/prepareforrsem/environment.yml +++ b/modules/nf-core/umitools/prepareforrsem/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::umi_tools=1.1.5 + - bioconda::umi_tools diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 0c9cbb101..fbf281f50 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -6,6 +6,6 @@ channels: - defaults dependencies: - - conda-forge::grep=3.11 - - conda-forge::sed=4.7 - - conda-forge::tar=1.34 + - conda-forge::grep + - conda-forge::sed + - conda-forge::tar diff --git a/nextflow.config b/nextflow.config index ca0d3a7e6..1164e2542 100644 --- a/nextflow.config +++ b/nextflow.config @@ -123,7 +123,7 @@ params { // Max resource options // Defaults only, expecting to be overwritten - max_memory = '128.GB' + max_memory = '256.GB' max_cpus = 16 max_time = '240.h' diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index b679a4b34..13c5bf118 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -142,7 +142,7 @@ workflow RNASEQ { .reads .mix(ch_fastq.single) .set { ch_cat_fastq } - ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first()) // // SUBWORKFLOW: Read QC, extract UMI and trim adapters with TrimGalore! From 4bdae48230c5b1bc9f8c0cdbdecce342f8ecb4cf Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 12:50:30 +0100 Subject: [PATCH 02/40] Fix up config --- conf/arm.config | 146 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 146 insertions(+) create mode 100644 conf/arm.config diff --git a/conf/arm.config b/conf/arm.config new file mode 100644 index 000000000..345e38efd --- /dev/null +++ b/conf/arm.config @@ -0,0 +1,146 @@ +// Apply software overrides for ARM compatibility + +withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { + conda = 'seqera::star=2.6.1d bioconda::samtools conda-forge::gawk=5.1.0' +} + +withName: 'STAR_GENOMEGENERATE_IGENOMES' { + conda = 'bioconda::star bioconda::samtools conda-forge::gawk=5.1.0' +} + +withName: 'BBSPLIT' { + conda = 'bioconda::bbmap' +} + +withName: 'BEDTOOLS_GENOMECOV' { + conda = 'bioconda::bedtools' +} + +withName: 'CAT_FASTQ' { + conda = 'conda-forge::coreutils' +} + +withName: 'CAT_ADDITIONAL_FASTA' { + conda = 'conda-forge::python' +} + +withName: 'CUSTOM_GETCHROMSIZES' { + conda = 'bioconda::samtools' +} + +withName: 'CUSTOM_TX2GENE' { + conda = 'python' +} + +withName: 'DUPRADAR' { + conda = 'bioconda::bioconductor-dupradar' +} + +withName: 'FASTP' { + conda = 'bioconda::fastp' +} + +withName: 'FQ_SUBSAMPLE' { + conda = 'bioconda::fq' +} + +withName: 'GFFREAD' { + conda = 'bioconda::gffread' +} + +withName: 'GUNZIP' { + conda = 'conda-forge::sed' +} + +withName: 'HISAT2_ALIGN' { + conda = 'bioconda::hisat2 bioconda::samtools' +} + +withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { + conda = 'bioconda::hisat2' +} + +withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { + conda = 'bioconda::kallisto' +} + +withName: 'MULTIQC' { + conda = 'bioconda::multiqc' +} + +withName: 'PICARD_MARKDUPLICATES' { + conda = 'bioconda::picard' +} + +withName: 'PRESEQ_LCEXTRAP' { + conda = 'bioconda::preseq' +} + +withName: 'QUALIMAP_RNASEQ' { + conda = 'bioconda::qualimap' +} + +withName: 'RSEM_CALCULATEEXPRESSION' { + conda = 'bioconda::rsem bioconda::star' +} + +withName: 'RSEM_PREPAREREFERENCE' { + conda = 'seqera::rsem seqera::star=2.6.1d' +} + +withName: 'RSEQC_BAMSTAT|RSEQC_INFEREXPERIMENT|RSEQC_INNERDISTANCE|RSEQC_JUNCTIONANNOTATION|RSEQC_JUNCTIONSATURATION|RSEQC_READDISTRIBUTION|RSEQC_READDUPLICATION|RSEQC_TIN' { + conda = 'bioconda::rseqc conda-forge::r-base' +} + +withName: 'SALMON_INDEX|SALMON_QUANT' { + conda = 'bioconda::salmon' +} + +withName: 'SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_INDEX|SAMTOOLS_SORT|SAMTOOLS_STATS' { + conda = 'bioconda::samtools bioconda::htslib' +} + +withName: 'SORTMERNA' { + conda = 'bioconda::sortmerna' +} + +withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { + conda = 'bioconda::star bioconda::samtools bioconda::htslib conda-forge::gawk' +} + +withName: 'STRINGTIE_STRINGTIE' { + conda = 'bioconda::stringtie' +} + +withName: 'SUBREAD_FEATURECOUNTS' { + conda = 'bioconda::subread' +} + +withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { + conda = 'bioconda::bioconductor-summarizedexperiment' +} + +withName: 'TXIMETA_TXIMPORT' { + conda = 'bioconda::bioconductor-tximeta' +} + +withName: 'TRIMGALORE' { + conda = 'bioconda::trim-galore bioconda::cutadapt' +} + +withName: 'UCSC_BEDCLIP' { + conda = 'bioconda::ucsc-bedclip' +} + +withName: 'UCSC_BEDGRAPHTOBIGWIG' { + conda = 'bioconda::ucsc-bedgraphtobigwig' +} + +withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { + conda = 'bioconda::umi_tools' +} + +withName: 'UNTAR' { + conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' +} + From c9d616ba7c72eb0eae9ebeec5c44eaa9cd6529d2 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 12:52:30 +0100 Subject: [PATCH 03/40] Reset environment ymls --- modules/nf-core/bbmap/bbsplit/environment.yml | 2 +- modules/nf-core/bedtools/genomecov/environment.yml | 3 +-- modules/nf-core/cat/fastq/environment.yml | 2 +- modules/nf-core/custom/catadditionalfasta/environment.yml | 2 +- modules/nf-core/custom/getchromsizes/environment.yml | 3 ++- modules/nf-core/custom/tx2gene/environment.yml | 2 +- modules/nf-core/dupradar/environment.yml | 2 +- modules/nf-core/fastp/environment.yml | 2 +- modules/nf-core/fastqc/environment.yml | 2 +- modules/nf-core/fq/subsample/environment.yml | 2 +- modules/nf-core/gffread/environment.yml | 2 +- modules/nf-core/gunzip/environment.yml | 4 +++- modules/nf-core/hisat2/align/environment.yml | 4 ++-- modules/nf-core/hisat2/build/environment.yml | 2 +- modules/nf-core/hisat2/extractsplicesites/environment.yml | 2 +- modules/nf-core/kallisto/index/environment.yml | 2 +- modules/nf-core/kallisto/quant/environment.yml | 2 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/picard/markduplicates/environment.yml | 2 +- modules/nf-core/preseq/lcextrap/environment.yml | 2 +- modules/nf-core/qualimap/rnaseq/environment.yml | 2 +- modules/nf-core/rsem/calculateexpression/environment.yml | 5 ++--- modules/nf-core/rsem/preparereference/environment.yml | 5 ++--- modules/nf-core/rseqc/bamstat/environment.yml | 4 ++-- modules/nf-core/rseqc/inferexperiment/environment.yml | 4 ++-- modules/nf-core/rseqc/innerdistance/environment.yml | 4 ++-- modules/nf-core/rseqc/junctionannotation/environment.yml | 4 ++-- modules/nf-core/rseqc/junctionsaturation/environment.yml | 4 ++-- modules/nf-core/rseqc/readdistribution/environment.yml | 4 ++-- modules/nf-core/rseqc/readduplication/environment.yml | 4 ++-- modules/nf-core/rseqc/tin/environment.yml | 4 ++-- modules/nf-core/salmon/index/environment.yml | 2 +- modules/nf-core/salmon/quant/environment.yml | 2 +- modules/nf-core/samtools/flagstat/environment.yml | 4 ++-- modules/nf-core/samtools/idxstats/environment.yml | 4 ++-- modules/nf-core/samtools/index/environment.yml | 4 ++-- modules/nf-core/samtools/sort/environment.yml | 4 ++-- modules/nf-core/samtools/stats/environment.yml | 4 ++-- modules/nf-core/sortmerna/environment.yml | 2 +- modules/nf-core/star/align/environment.yml | 8 ++++---- modules/nf-core/star/genomegenerate/environment.yml | 8 ++++---- modules/nf-core/stringtie/stringtie/environment.yml | 2 +- modules/nf-core/subread/featurecounts/environment.yml | 2 +- .../summarizedexperiment/environment.yml | 2 +- modules/nf-core/trimgalore/environment.yml | 4 ++-- modules/nf-core/tximeta/tximport/environment.yml | 2 +- modules/nf-core/ucsc/bedclip/environment.yml | 2 +- modules/nf-core/ucsc/bedgraphtobigwig/environment.yml | 2 +- modules/nf-core/umitools/dedup/environment.yml | 2 +- modules/nf-core/umitools/extract/environment.yml | 2 +- modules/nf-core/umitools/prepareforrsem/environment.yml | 2 +- modules/nf-core/untar/environment.yml | 6 +++--- 52 files changed, 80 insertions(+), 80 deletions(-) diff --git a/modules/nf-core/bbmap/bbsplit/environment.yml b/modules/nf-core/bbmap/bbsplit/environment.yml index 3a0ecdf34..dfd8936e1 100644 --- a/modules/nf-core/bbmap/bbsplit/environment.yml +++ b/modules/nf-core/bbmap/bbsplit/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bbmap + - bioconda::bbmap=39.01 diff --git a/modules/nf-core/bedtools/genomecov/environment.yml b/modules/nf-core/bedtools/genomecov/environment.yml index d415ae6ec..5683bc05f 100644 --- a/modules/nf-core/bedtools/genomecov/environment.yml +++ b/modules/nf-core/bedtools/genomecov/environment.yml @@ -1,6 +1,5 @@ channels: - - seqera - conda-forge - bioconda dependencies: - - bioconda::bedtools + - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index d15cbda27..c7eb9bd1c 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::coreutils + - conda-forge::coreutils=8.30 diff --git a/modules/nf-core/custom/catadditionalfasta/environment.yml b/modules/nf-core/custom/catadditionalfasta/environment.yml index fd1010315..1d80d11a9 100644 --- a/modules/nf-core/custom/catadditionalfasta/environment.yml +++ b/modules/nf-core/custom/catadditionalfasta/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::python" \ No newline at end of file + - conda-forge::python=3.9.5 diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml index 96b17c413..da2df5e43 100644 --- a/modules/nf-core/custom/getchromsizes/environment.yml +++ b/modules/nf-core/custom/getchromsizes/environment.yml @@ -2,4 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools \ No newline at end of file + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/custom/tx2gene/environment.yml b/modules/nf-core/custom/tx2gene/environment.yml index f626c1c72..9f5f9fb9b 100644 --- a/modules/nf-core/custom/tx2gene/environment.yml +++ b/modules/nf-core/custom/tx2gene/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - python + - python=3.9.5 diff --git a/modules/nf-core/dupradar/environment.yml b/modules/nf-core/dupradar/environment.yml index ca8f5abef..fb16938d2 100644 --- a/modules/nf-core/dupradar/environment.yml +++ b/modules/nf-core/dupradar/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bioconductor-dupradar" + - "bioconda::bioconductor-dupradar=1.32.0" diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml index de3512e0a..26d4aca5d 100644 --- a/modules/nf-core/fastp/environment.yml +++ b/modules/nf-core/fastp/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fastp + - bioconda::fastp=0.23.4 diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 30e0b77e3..691d4c763 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fastqc + - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fq/subsample/environment.yml b/modules/nf-core/fq/subsample/environment.yml index f28625955..eaba9339b 100644 --- a/modules/nf-core/fq/subsample/environment.yml +++ b/modules/nf-core/fq/subsample/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fq + - bioconda::fq=0.9.1 diff --git a/modules/nf-core/gffread/environment.yml b/modules/nf-core/gffread/environment.yml index 61b39921a..ee2398416 100644 --- a/modules/nf-core/gffread/environment.yml +++ b/modules/nf-core/gffread/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gffread \ No newline at end of file + - bioconda::gffread=0.12.7 diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml index 86c0feb98..c7794856d 100644 --- a/modules/nf-core/gunzip/environment.yml +++ b/modules/nf-core/gunzip/environment.yml @@ -2,4 +2,6 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::sed \ No newline at end of file + - conda-forge::grep=3.11 + - conda-forge::sed=4.8 + - conda-forge::tar=1.34 diff --git a/modules/nf-core/hisat2/align/environment.yml b/modules/nf-core/hisat2/align/environment.yml index 75a1d7505..26c62a3bf 100644 --- a/modules/nf-core/hisat2/align/environment.yml +++ b/modules/nf-core/hisat2/align/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::hisat2 - - bioconda::samtools + - bioconda::hisat2=2.2.1 + - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/hisat2/build/environment.yml b/modules/nf-core/hisat2/build/environment.yml index c2696c30e..afced7338 100644 --- a/modules/nf-core/hisat2/build/environment.yml +++ b/modules/nf-core/hisat2/build/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::hisat2 + - bioconda::hisat2=2.2.1 diff --git a/modules/nf-core/hisat2/extractsplicesites/environment.yml b/modules/nf-core/hisat2/extractsplicesites/environment.yml index c2696c30e..afced7338 100644 --- a/modules/nf-core/hisat2/extractsplicesites/environment.yml +++ b/modules/nf-core/hisat2/extractsplicesites/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::hisat2 + - bioconda::hisat2=2.2.1 diff --git a/modules/nf-core/kallisto/index/environment.yml b/modules/nf-core/kallisto/index/environment.yml index 6ccef310c..27be64918 100644 --- a/modules/nf-core/kallisto/index/environment.yml +++ b/modules/nf-core/kallisto/index/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::kallisto + - bioconda::kallisto=0.48.0 diff --git a/modules/nf-core/kallisto/quant/environment.yml b/modules/nf-core/kallisto/quant/environment.yml index 6ccef310c..27be64918 100644 --- a/modules/nf-core/kallisto/quant/environment.yml +++ b/modules/nf-core/kallisto/quant/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::kallisto + - bioconda::kallisto=0.48.0 diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 103b4c045..6f5b867b7 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc \ No newline at end of file + - bioconda::multiqc=1.25.1 diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml index 4dc4357d0..5f919a9a9 100644 --- a/modules/nf-core/picard/markduplicates/environment.yml +++ b/modules/nf-core/picard/markduplicates/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard + - bioconda::picard=3.1.1 diff --git a/modules/nf-core/preseq/lcextrap/environment.yml b/modules/nf-core/preseq/lcextrap/environment.yml index 06bec39d0..926d7aece 100644 --- a/modules/nf-core/preseq/lcextrap/environment.yml +++ b/modules/nf-core/preseq/lcextrap/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::preseq + - bioconda::preseq=3.1.2 diff --git a/modules/nf-core/qualimap/rnaseq/environment.yml b/modules/nf-core/qualimap/rnaseq/environment.yml index 28bab2f99..4fa5f4e8e 100644 --- a/modules/nf-core/qualimap/rnaseq/environment.yml +++ b/modules/nf-core/qualimap/rnaseq/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::qualimap + - bioconda::qualimap=2.3 diff --git a/modules/nf-core/rsem/calculateexpression/environment.yml b/modules/nf-core/rsem/calculateexpression/environment.yml index b29ff989b..bcf70fa9a 100644 --- a/modules/nf-core/rsem/calculateexpression/environment.yml +++ b/modules/nf-core/rsem/calculateexpression/environment.yml @@ -1,7 +1,6 @@ channels: - - seqera - conda-forge - bioconda dependencies: - - bioconda::rsem - - bioconda::star + - bioconda::rsem=1.3.3 + - bioconda::star=2.7.10a diff --git a/modules/nf-core/rsem/preparereference/environment.yml b/modules/nf-core/rsem/preparereference/environment.yml index b70d9f18d..bcf70fa9a 100644 --- a/modules/nf-core/rsem/preparereference/environment.yml +++ b/modules/nf-core/rsem/preparereference/environment.yml @@ -1,7 +1,6 @@ channels: - - seqera - conda-forge - bioconda dependencies: - - seqera::rsem - - seqera::star=2.6.1d + - bioconda::rsem=1.3.3 + - bioconda::star=2.7.10a diff --git a/modules/nf-core/rseqc/bamstat/environment.yml b/modules/nf-core/rseqc/bamstat/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/bamstat/environment.yml +++ b/modules/nf-core/rseqc/bamstat/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/inferexperiment/environment.yml b/modules/nf-core/rseqc/inferexperiment/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/inferexperiment/environment.yml +++ b/modules/nf-core/rseqc/inferexperiment/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/innerdistance/environment.yml b/modules/nf-core/rseqc/innerdistance/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/innerdistance/environment.yml +++ b/modules/nf-core/rseqc/innerdistance/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/junctionannotation/environment.yml b/modules/nf-core/rseqc/junctionannotation/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/junctionannotation/environment.yml +++ b/modules/nf-core/rseqc/junctionannotation/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/junctionsaturation/environment.yml b/modules/nf-core/rseqc/junctionsaturation/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/junctionsaturation/environment.yml +++ b/modules/nf-core/rseqc/junctionsaturation/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/readdistribution/environment.yml b/modules/nf-core/rseqc/readdistribution/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/readdistribution/environment.yml +++ b/modules/nf-core/rseqc/readdistribution/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/readduplication/environment.yml b/modules/nf-core/rseqc/readduplication/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/readduplication/environment.yml +++ b/modules/nf-core/rseqc/readduplication/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/tin/environment.yml b/modules/nf-core/rseqc/tin/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/tin/environment.yml +++ b/modules/nf-core/rseqc/tin/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/salmon/index/environment.yml b/modules/nf-core/salmon/index/environment.yml index b4e2d89de..471164faa 100644 --- a/modules/nf-core/salmon/index/environment.yml +++ b/modules/nf-core/salmon/index/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::salmon + - bioconda::salmon=1.10.1 diff --git a/modules/nf-core/salmon/quant/environment.yml b/modules/nf-core/salmon/quant/environment.yml index b4e2d89de..471164faa 100644 --- a/modules/nf-core/salmon/quant/environment.yml +++ b/modules/nf-core/salmon/quant/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::salmon + - bioconda::salmon=1.10.1 diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index 55c7b199f..da2df5e43 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools - - bioconda::htslib \ No newline at end of file + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index 55c7b199f..da2df5e43 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools - - bioconda::htslib \ No newline at end of file + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 55c7b199f..da2df5e43 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools - - bioconda::htslib \ No newline at end of file + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index 55c7b199f..da2df5e43 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools - - bioconda::htslib \ No newline at end of file + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index 55c7b199f..da2df5e43 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools - - bioconda::htslib \ No newline at end of file + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/sortmerna/environment.yml b/modules/nf-core/sortmerna/environment.yml index 6fd5e7442..fab44081f 100644 --- a/modules/nf-core/sortmerna/environment.yml +++ b/modules/nf-core/sortmerna/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sortmerna + - bioconda::sortmerna=4.3.6 diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml index 0084b66ae..e3d1c714d 100644 --- a/modules/nf-core/star/align/environment.yml +++ b/modules/nf-core/star/align/environment.yml @@ -2,7 +2,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::star - - bioconda::samtools - - bioconda::htslib - - conda-forge::gawk + - bioconda::star=2.7.10a + - bioconda::samtools=1.18 + - bioconda::htslib=1.18 + - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml index 6617b4720..38611dfa2 100644 --- a/modules/nf-core/star/genomegenerate/environment.yml +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -2,7 +2,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools - - bioconda::htslib - - bioconda::star - - conda-forge::gawk + - bioconda::samtools=1.18 + - bioconda::htslib=1.18 + - bioconda::star=2.7.10a + - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/stringtie/stringtie/environment.yml b/modules/nf-core/stringtie/stringtie/environment.yml index 25e1a3810..0556de41a 100644 --- a/modules/nf-core/stringtie/stringtie/environment.yml +++ b/modules/nf-core/stringtie/stringtie/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::stringtie + - bioconda::stringtie=2.2.1 diff --git a/modules/nf-core/subread/featurecounts/environment.yml b/modules/nf-core/subread/featurecounts/environment.yml index 43bff6526..7e919aa31 100644 --- a/modules/nf-core/subread/featurecounts/environment.yml +++ b/modules/nf-core/subread/featurecounts/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::subread + - bioconda::subread=2.0.1 diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml index 24ce1dcde..dc4e6c936 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bioconductor-summarizedexperiment" + - "bioconda::bioconductor-summarizedexperiment=1.32.0" diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml index c83091ea1..f172c1b39 100644 --- a/modules/nf-core/trimgalore/environment.yml +++ b/modules/nf-core/trimgalore/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::trim-galore - - bioconda::cutadapt \ No newline at end of file + - bioconda::cutadapt=3.4 + - bioconda::trim-galore=0.6.7 diff --git a/modules/nf-core/tximeta/tximport/environment.yml b/modules/nf-core/tximeta/tximport/environment.yml index 5c5179f35..4b6df0cfe 100644 --- a/modules/nf-core/tximeta/tximport/environment.yml +++ b/modules/nf-core/tximeta/tximport/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bioconductor-tximeta" + - "bioconda::bioconductor-tximeta=1.20.1" diff --git a/modules/nf-core/ucsc/bedclip/environment.yml b/modules/nf-core/ucsc/bedclip/environment.yml index 8e6772864..94e825f03 100644 --- a/modules/nf-core/ucsc/bedclip/environment.yml +++ b/modules/nf-core/ucsc/bedclip/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ucsc-bedclip + - bioconda::ucsc-bedclip=377 diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml index 7eca50fcc..a54fb8f16 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml +++ b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ucsc-bedgraphtobigwig + - bioconda::ucsc-bedgraphtobigwig=445 diff --git a/modules/nf-core/umitools/dedup/environment.yml b/modules/nf-core/umitools/dedup/environment.yml index 2d4e5317c..9f9e03c49 100644 --- a/modules/nf-core/umitools/dedup/environment.yml +++ b/modules/nf-core/umitools/dedup/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::umi_tools + - bioconda::umi_tools=1.1.5 diff --git a/modules/nf-core/umitools/extract/environment.yml b/modules/nf-core/umitools/extract/environment.yml index 2d4e5317c..9f9e03c49 100644 --- a/modules/nf-core/umitools/extract/environment.yml +++ b/modules/nf-core/umitools/extract/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::umi_tools + - bioconda::umi_tools=1.1.5 diff --git a/modules/nf-core/umitools/prepareforrsem/environment.yml b/modules/nf-core/umitools/prepareforrsem/environment.yml index 2d4e5317c..9f9e03c49 100644 --- a/modules/nf-core/umitools/prepareforrsem/environment.yml +++ b/modules/nf-core/umitools/prepareforrsem/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::umi_tools + - bioconda::umi_tools=1.1.5 diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 14e237118..c7794856d 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -2,6 +2,6 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::grep - - conda-forge::sed - - conda-forge::tar \ No newline at end of file + - conda-forge::grep=3.11 + - conda-forge::sed=4.8 + - conda-forge::tar=1.34 From 9f640ab5a1b517a0bdd6cb43a9eac5a364edbc4b Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 12:55:16 +0100 Subject: [PATCH 04/40] Reset main.nfs with software changes only --- modules/local/star_align_igenomes/main.nf | 2 +- modules/local/star_genomegenerate_igenomes/main.nf | 2 +- modules/nf-core/bedtools/genomecov/main.nf | 1 - 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/modules/local/star_align_igenomes/main.nf b/modules/local/star_align_igenomes/main.nf index 7341d5778..7bda3df84 100644 --- a/modules/local/star_align_igenomes/main.nf +++ b/modules/local/star_align_igenomes/main.nf @@ -2,7 +2,7 @@ process STAR_ALIGN_IGENOMES { tag "$meta.id" label 'process_high' - conda "seqera::star=2.6.1d bioconda::samtools conda-forge::gawk=5.1.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' : 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }" diff --git a/modules/local/star_genomegenerate_igenomes/main.nf b/modules/local/star_genomegenerate_igenomes/main.nf index 775afde95..4e2fcf6bf 100644 --- a/modules/local/star_genomegenerate_igenomes/main.nf +++ b/modules/local/star_genomegenerate_igenomes/main.nf @@ -2,7 +2,7 @@ process STAR_GENOMEGENERATE_IGENOMES { tag "$fasta" label 'process_high' - conda "bioconda::star bioconda::samtools conda-forge::gawk=5.1.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' : 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }" diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 98cfd4c8e..91869ec23 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -27,7 +27,6 @@ process BEDTOOLS_GENOMECOV { if (!args_list.contains('-bg') && (scale > 0 && scale != 1)) { args += " -bg" } - // Sorts output file by chromosome and position using additional options for performance and consistency // See https://www.biostars.org/p/66927/ for further details def buffer = task.memory ? "--buffer-size=${task.memory.toGiga().intdiv(2)}G" : '' From 00cff4c8e48a4cd15bd3fdb9ab92c0bfb2ae141e Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 12:58:29 +0100 Subject: [PATCH 05/40] Link sw configs to arm profile --- nextflow.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow.config b/nextflow.config index 496a9429f..525c6f4e1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -186,6 +186,7 @@ profiles { } arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + includeConfig 'conf/arm.config' } singularity { singularity.enabled = true From f281e0b13f63fda6b7a984910ff5db8ce665d072 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 13:13:27 +0100 Subject: [PATCH 06/40] Add process block --- conf/arm.config | 294 ++++++++++++++++++++++++------------------------ 1 file changed, 148 insertions(+), 146 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 345e38efd..112cb66af 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -1,146 +1,148 @@ -// Apply software overrides for ARM compatibility - -withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { - conda = 'seqera::star=2.6.1d bioconda::samtools conda-forge::gawk=5.1.0' -} - -withName: 'STAR_GENOMEGENERATE_IGENOMES' { - conda = 'bioconda::star bioconda::samtools conda-forge::gawk=5.1.0' -} - -withName: 'BBSPLIT' { - conda = 'bioconda::bbmap' -} - -withName: 'BEDTOOLS_GENOMECOV' { - conda = 'bioconda::bedtools' -} - -withName: 'CAT_FASTQ' { - conda = 'conda-forge::coreutils' -} - -withName: 'CAT_ADDITIONAL_FASTA' { - conda = 'conda-forge::python' -} - -withName: 'CUSTOM_GETCHROMSIZES' { - conda = 'bioconda::samtools' -} - -withName: 'CUSTOM_TX2GENE' { - conda = 'python' -} - -withName: 'DUPRADAR' { - conda = 'bioconda::bioconductor-dupradar' -} - -withName: 'FASTP' { - conda = 'bioconda::fastp' -} - -withName: 'FQ_SUBSAMPLE' { - conda = 'bioconda::fq' -} - -withName: 'GFFREAD' { - conda = 'bioconda::gffread' -} - -withName: 'GUNZIP' { - conda = 'conda-forge::sed' -} - -withName: 'HISAT2_ALIGN' { - conda = 'bioconda::hisat2 bioconda::samtools' -} - -withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { - conda = 'bioconda::hisat2' -} - -withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { - conda = 'bioconda::kallisto' -} - -withName: 'MULTIQC' { - conda = 'bioconda::multiqc' -} - -withName: 'PICARD_MARKDUPLICATES' { - conda = 'bioconda::picard' -} - -withName: 'PRESEQ_LCEXTRAP' { - conda = 'bioconda::preseq' -} - -withName: 'QUALIMAP_RNASEQ' { - conda = 'bioconda::qualimap' -} - -withName: 'RSEM_CALCULATEEXPRESSION' { - conda = 'bioconda::rsem bioconda::star' -} - -withName: 'RSEM_PREPAREREFERENCE' { - conda = 'seqera::rsem seqera::star=2.6.1d' -} - -withName: 'RSEQC_BAMSTAT|RSEQC_INFEREXPERIMENT|RSEQC_INNERDISTANCE|RSEQC_JUNCTIONANNOTATION|RSEQC_JUNCTIONSATURATION|RSEQC_READDISTRIBUTION|RSEQC_READDUPLICATION|RSEQC_TIN' { - conda = 'bioconda::rseqc conda-forge::r-base' -} - -withName: 'SALMON_INDEX|SALMON_QUANT' { - conda = 'bioconda::salmon' -} - -withName: 'SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_INDEX|SAMTOOLS_SORT|SAMTOOLS_STATS' { - conda = 'bioconda::samtools bioconda::htslib' -} - -withName: 'SORTMERNA' { - conda = 'bioconda::sortmerna' -} - -withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { - conda = 'bioconda::star bioconda::samtools bioconda::htslib conda-forge::gawk' -} - -withName: 'STRINGTIE_STRINGTIE' { - conda = 'bioconda::stringtie' -} - -withName: 'SUBREAD_FEATURECOUNTS' { - conda = 'bioconda::subread' -} - -withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { - conda = 'bioconda::bioconductor-summarizedexperiment' -} - -withName: 'TXIMETA_TXIMPORT' { - conda = 'bioconda::bioconductor-tximeta' -} - -withName: 'TRIMGALORE' { - conda = 'bioconda::trim-galore bioconda::cutadapt' -} - -withName: 'UCSC_BEDCLIP' { - conda = 'bioconda::ucsc-bedclip' -} - -withName: 'UCSC_BEDGRAPHTOBIGWIG' { - conda = 'bioconda::ucsc-bedgraphtobigwig' -} - -withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { - conda = 'bioconda::umi_tools' -} - -withName: 'UNTAR' { - conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' -} - +process { + + // Apply software overrides for ARM compatibility + + withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { + conda = 'seqera::star=2.6.1d bioconda::samtools conda-forge::gawk=5.1.0' + } + + withName: 'STAR_GENOMEGENERATE_IGENOMES' { + conda = 'bioconda::star bioconda::samtools conda-forge::gawk=5.1.0' + } + + withName: 'BBSPLIT' { + conda = 'bioconda::bbmap' + } + + withName: 'BEDTOOLS_GENOMECOV' { + conda = 'bioconda::bedtools' + } + + withName: 'CAT_FASTQ' { + conda = 'conda-forge::coreutils' + } + + withName: 'CAT_ADDITIONAL_FASTA' { + conda = 'conda-forge::python' + } + + withName: 'CUSTOM_GETCHROMSIZES' { + conda = 'bioconda::samtools' + } + + withName: 'CUSTOM_TX2GENE' { + conda = 'python' + } + + withName: 'DUPRADAR' { + conda = 'bioconda::bioconductor-dupradar' + } + + withName: 'FASTP' { + conda = 'bioconda::fastp' + } + + withName: 'FQ_SUBSAMPLE' { + conda = 'bioconda::fq' + } + + withName: 'GFFREAD' { + conda = 'bioconda::gffread' + } + + withName: 'GUNZIP' { + conda = 'conda-forge::sed' + } + + withName: 'HISAT2_ALIGN' { + conda = 'bioconda::hisat2 bioconda::samtools' + } + + withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { + conda = 'bioconda::hisat2' + } + + withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { + conda = 'bioconda::kallisto' + } + + withName: 'MULTIQC' { + conda = 'bioconda::multiqc' + } + + withName: 'PICARD_MARKDUPLICATES' { + conda = 'bioconda::picard' + } + + withName: 'PRESEQ_LCEXTRAP' { + conda = 'bioconda::preseq' + } + + withName: 'QUALIMAP_RNASEQ' { + conda = 'bioconda::qualimap' + } + + withName: 'RSEM_CALCULATEEXPRESSION' { + conda = 'bioconda::rsem bioconda::star' + } + + withName: 'RSEM_PREPAREREFERENCE' { + conda = 'seqera::rsem seqera::star=2.6.1d' + } + + withName: 'RSEQC_BAMSTAT|RSEQC_INFEREXPERIMENT|RSEQC_INNERDISTANCE|RSEQC_JUNCTIONANNOTATION|RSEQC_JUNCTIONSATURATION|RSEQC_READDISTRIBUTION|RSEQC_READDUPLICATION|RSEQC_TIN' { + conda = 'bioconda::rseqc conda-forge::r-base' + } + + withName: 'SALMON_INDEX|SALMON_QUANT' { + conda = 'bioconda::salmon' + } + + withName: 'SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_INDEX|SAMTOOLS_SORT|SAMTOOLS_STATS' { + conda = 'bioconda::samtools bioconda::htslib' + } + + withName: 'SORTMERNA' { + conda = 'bioconda::sortmerna' + } + + withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { + conda = 'bioconda::star bioconda::samtools bioconda::htslib conda-forge::gawk' + } + + withName: 'STRINGTIE_STRINGTIE' { + conda = 'bioconda::stringtie' + } + + withName: 'SUBREAD_FEATURECOUNTS' { + conda = 'bioconda::subread' + } + + withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { + conda = 'bioconda::bioconductor-summarizedexperiment' + } + + withName: 'TXIMETA_TXIMPORT' { + conda = 'bioconda::bioconductor-tximeta' + } + + withName: 'TRIMGALORE' { + conda = 'bioconda::trim-galore bioconda::cutadapt' + } + + withName: 'UCSC_BEDCLIP' { + conda = 'bioconda::ucsc-bedclip' + } + + withName: 'UCSC_BEDGRAPHTOBIGWIG' { + conda = 'bioconda::ucsc-bedgraphtobigwig' + } + + withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { + conda = 'bioconda::umi_tools' + } + + withName: 'UNTAR' { + conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' + } +} From f5208dd0e78762e51bb34740ecea16a5cfc40949 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 16:31:04 +0100 Subject: [PATCH 07/40] note pins --- conf/arm.config | 76 ++++++++++++++++++++++++++++++++++++------------- 1 file changed, 56 insertions(+), 20 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 112cb66af..d5cbad5b4 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -3,146 +3,182 @@ process { // Apply software overrides for ARM compatibility withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { - conda = 'seqera::star=2.6.1d bioconda::samtools conda-forge::gawk=5.1.0' + conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' + //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' } withName: 'STAR_GENOMEGENERATE_IGENOMES' { - conda = 'bioconda::star bioconda::samtools conda-forge::gawk=5.1.0' + conda = 'bioconda::star bioconda::samtools=1.21 conda-forge::gawk=5.1.0' + //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' } withName: 'BBSPLIT' { - conda = 'bioconda::bbmap' + conda = 'bioconda::bbmap' + // conda = 'bioconda::bbmap=39.01' } withName: 'BEDTOOLS_GENOMECOV' { - conda = 'bioconda::bedtools' + conda = 'bioconda::bedtools::2.13.1' + //conda = 'bioconda::bedtools::2.13.1' } withName: 'CAT_FASTQ' { conda = 'conda-forge::coreutils' + //conda = 'conda-forge::coreutils=8.30' } withName: 'CAT_ADDITIONAL_FASTA' { conda = 'conda-forge::python' + //conda = 'conda-forge::coreutils=3.9.5' } withName: 'CUSTOM_GETCHROMSIZES' { - conda = 'bioconda::samtools' + conda = 'bioconda::samtools=1.21' + //conda = 'bioconda::samtools=1.20 bioconda::htslib=1.20' } withName: 'CUSTOM_TX2GENE' { - conda = 'python' + conda = 'python=3.13.0' + //conda = 'python=3.9.5' } withName: 'DUPRADAR' { - conda = 'bioconda::bioconductor-dupradar' + conda = 'bioconda::bioconductor-dupradar=1.32.0' + //conda = 'bioconda::bioconductor-dupradar=1.32.0' } withName: 'FASTP' { conda = 'bioconda::fastp' + //conda = 'bioconda::fastp=0.23.4' } withName: 'FQ_SUBSAMPLE' { conda = 'bioconda::fq' + //conda = 'bioconda::fq=0.9.1' } withName: 'GFFREAD' { conda = 'bioconda::gffread' + //conda = 'bioconda::gffread=0.12.7' } withName: 'GUNZIP' { conda = 'conda-forge::sed' + //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' } withName: 'HISAT2_ALIGN' { conda = 'bioconda::hisat2 bioconda::samtools' + //conda = 'bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1' } withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { conda = 'bioconda::hisat2' + //conda = 'bioconda::hisat2=2.2.1' } withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { conda = 'bioconda::kallisto' + //conda = 'bioconda::kallisto=0.48.0' } withName: 'MULTIQC' { - conda = 'bioconda::multiqc' + conda = 'bioconda::multiqc=1.25.1' + //conda = 'bioconda::multiqc=1.25.1' } withName: 'PICARD_MARKDUPLICATES' { - conda = 'bioconda::picard' + conda = 'bioconda::picard=3.3.0' + //conda = 'bioconda::picard=3.1.1' } withName: 'PRESEQ_LCEXTRAP' { conda = 'bioconda::preseq' + //conda = 'bioconda::preseq=3.1.2' } withName: 'QUALIMAP_RNASEQ' { - conda = 'bioconda::qualimap' + conda = 'bioconda::qualimap=2.3' + //conda = 'bioconda::qualimap=2.3' } withName: 'RSEM_CALCULATEEXPRESSION' { conda = 'bioconda::rsem bioconda::star' + //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' } withName: 'RSEM_PREPAREREFERENCE' { conda = 'seqera::rsem seqera::star=2.6.1d' + //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' } withName: 'RSEQC_BAMSTAT|RSEQC_INFEREXPERIMENT|RSEQC_INNERDISTANCE|RSEQC_JUNCTIONANNOTATION|RSEQC_JUNCTIONSATURATION|RSEQC_READDISTRIBUTION|RSEQC_READDUPLICATION|RSEQC_TIN' { - conda = 'bioconda::rseqc conda-forge::r-base' + conda = 'bioconda::rseqc=5.0.2 conda-forge::r-base' + //conda = 'bioconda::rseqc=5.0.3 conda-forge::r-base>=3.5' } withName: 'SALMON_INDEX|SALMON_QUANT' { - conda = 'bioconda::salmon' + conda = 'bioconda::salmon=1.10.3' + //conda = 'bioconda::salmon=1.10.1' } withName: 'SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_INDEX|SAMTOOLS_SORT|SAMTOOLS_STATS' { - conda = 'bioconda::samtools bioconda::htslib' + conda = 'bioconda::samtools=1.21 bioconda::htslib' + //conda = 'bioconda::samtools=1.20 bioconda::htslib' } withName: 'SORTMERNA' { conda = 'bioconda::sortmerna' + //conda = 'bioconda::sortmerna=4.3.6' } withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { conda = 'bioconda::star bioconda::samtools bioconda::htslib conda-forge::gawk' + //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' } withName: 'STRINGTIE_STRINGTIE' { - conda = 'bioconda::stringtie' + conda = 'bioconda::stringtie=2.2.3' + //conda = 'bioconda::stringtie=2.2.1' } withName: 'SUBREAD_FEATURECOUNTS' { - conda = 'bioconda::subread' + conda = 'bioconda::subread=2.0.6' + //conda = 'bioconda::subread=2.0.1' } withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { - conda = 'bioconda::bioconductor-summarizedexperiment' + conda = 'bioconda::bioconductor-summarizedexperiment=1.32.0' + //conda = 'bioconda::bioconductor-summarizedexperiment=1.32.0' } withName: 'TXIMETA_TXIMPORT' { - conda = 'bioconda::bioconductor-tximeta' + conda = 'bioconda::bioconductor-tximeta=1.20.1' + //conda = 'bioconda::bioconductor-tximeta=1.20.1' } withName: 'TRIMGALORE' { - conda = 'bioconda::trim-galore bioconda::cutadapt' + conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9' + //conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4' } withName: 'UCSC_BEDCLIP' { - conda = 'bioconda::ucsc-bedclip' + conda = 'bioconda::ucsc-bedclip=377' + //conda = 'bioconda::ucsc-bedclip=377' } withName: 'UCSC_BEDGRAPHTOBIGWIG' { - conda = 'bioconda::ucsc-bedgraphtobigwig' + conda = 'bioconda::ucsc-bedgraphtobigwig=445' + //conda = 'bioconda::ucsc-bedgraphtobigwig=445' } withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { conda = 'bioconda::umi_tools' + //conda = 'bioconda::umi_tools=1.1.5' } withName: 'UNTAR' { conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' + //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' } } From ea8b9e8be4657416a3041351718493af03bfd410 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 17:23:49 +0100 Subject: [PATCH 08/40] Remove conda overrides that were having no impact --- conf/arm.config | 40 ---------------------------------------- 1 file changed, 40 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index d5cbad5b4..d73605e09 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -17,11 +17,6 @@ process { // conda = 'bioconda::bbmap=39.01' } - withName: 'BEDTOOLS_GENOMECOV' { - conda = 'bioconda::bedtools::2.13.1' - //conda = 'bioconda::bedtools::2.13.1' - } - withName: 'CAT_FASTQ' { conda = 'conda-forge::coreutils' //conda = 'conda-forge::coreutils=8.30' @@ -42,11 +37,6 @@ process { //conda = 'python=3.9.5' } - withName: 'DUPRADAR' { - conda = 'bioconda::bioconductor-dupradar=1.32.0' - //conda = 'bioconda::bioconductor-dupradar=1.32.0' - } - withName: 'FASTP' { conda = 'bioconda::fastp' //conda = 'bioconda::fastp=0.23.4' @@ -82,11 +72,6 @@ process { //conda = 'bioconda::kallisto=0.48.0' } - withName: 'MULTIQC' { - conda = 'bioconda::multiqc=1.25.1' - //conda = 'bioconda::multiqc=1.25.1' - } - withName: 'PICARD_MARKDUPLICATES' { conda = 'bioconda::picard=3.3.0' //conda = 'bioconda::picard=3.1.1' @@ -97,11 +82,6 @@ process { //conda = 'bioconda::preseq=3.1.2' } - withName: 'QUALIMAP_RNASEQ' { - conda = 'bioconda::qualimap=2.3' - //conda = 'bioconda::qualimap=2.3' - } - withName: 'RSEM_CALCULATEEXPRESSION' { conda = 'bioconda::rsem bioconda::star' //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' @@ -147,31 +127,11 @@ process { //conda = 'bioconda::subread=2.0.1' } - withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { - conda = 'bioconda::bioconductor-summarizedexperiment=1.32.0' - //conda = 'bioconda::bioconductor-summarizedexperiment=1.32.0' - } - - withName: 'TXIMETA_TXIMPORT' { - conda = 'bioconda::bioconductor-tximeta=1.20.1' - //conda = 'bioconda::bioconductor-tximeta=1.20.1' - } - withName: 'TRIMGALORE' { conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9' //conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4' } - withName: 'UCSC_BEDCLIP' { - conda = 'bioconda::ucsc-bedclip=377' - //conda = 'bioconda::ucsc-bedclip=377' - } - - withName: 'UCSC_BEDGRAPHTOBIGWIG' { - conda = 'bioconda::ucsc-bedgraphtobigwig=445' - //conda = 'bioconda::ucsc-bedgraphtobigwig=445' - } - withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { conda = 'bioconda::umi_tools' //conda = 'bioconda::umi_tools=1.1.5' From db02d992556f593a66b0d5da9718f519bb2934f0 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 09:45:44 +0100 Subject: [PATCH 09/40] Use different RSEQC pin --- conf/arm.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/arm.config b/conf/arm.config index d73605e09..f8e288f9d 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -93,7 +93,7 @@ process { } withName: 'RSEQC_BAMSTAT|RSEQC_INFEREXPERIMENT|RSEQC_INNERDISTANCE|RSEQC_JUNCTIONANNOTATION|RSEQC_JUNCTIONSATURATION|RSEQC_READDISTRIBUTION|RSEQC_READDUPLICATION|RSEQC_TIN' { - conda = 'bioconda::rseqc=5.0.2 conda-forge::r-base' + conda = 'bioconda::rseqc=5.0.4 conda-forge::r-base' //conda = 'bioconda::rseqc=5.0.3 conda-forge::r-base>=3.5' } From 4a8ed2bb00bff13cdef9f4470c4a95bead441542 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 10:28:04 +0100 Subject: [PATCH 10/40] update BEDGRAPHTOBIGWIG pin --- conf/arm.config | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/conf/arm.config b/conf/arm.config index f8e288f9d..4f7772681 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -131,6 +131,11 @@ process { conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9' //conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4' } + + withName: 'UCSC_BEDGRAPHTOBIGWIG' { + conda = 'bioconda::ucsc-bedgraphtobigwig=469' + //conda = 'bioconda::ucsc-bedgraphtobigwig=469' + } withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { conda = 'bioconda::umi_tools' From b86a6f9d9fc3515865eb4aaa600882df6c893c80 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 10:37:14 +0100 Subject: [PATCH 11/40] Fix annotation --- conf/arm.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/arm.config b/conf/arm.config index 4f7772681..4efeabdfe 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -133,7 +133,7 @@ process { } withName: 'UCSC_BEDGRAPHTOBIGWIG' { - conda = 'bioconda::ucsc-bedgraphtobigwig=469' + conda = 'bioconda::ucsc-bedgraphtobigwig=445' //conda = 'bioconda::ucsc-bedgraphtobigwig=469' } From 1b96eb886b80c4cba0691728a89a4f17dbc5a0ec Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 10:47:36 +0100 Subject: [PATCH 12/40] Don't think we need the RSEQC pin --- conf/arm.config | 5 ----- 1 file changed, 5 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 4efeabdfe..37a6d1211 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -92,11 +92,6 @@ process { //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' } - withName: 'RSEQC_BAMSTAT|RSEQC_INFEREXPERIMENT|RSEQC_INNERDISTANCE|RSEQC_JUNCTIONANNOTATION|RSEQC_JUNCTIONSATURATION|RSEQC_READDISTRIBUTION|RSEQC_READDUPLICATION|RSEQC_TIN' { - conda = 'bioconda::rseqc=5.0.4 conda-forge::r-base' - //conda = 'bioconda::rseqc=5.0.3 conda-forge::r-base>=3.5' - } - withName: 'SALMON_INDEX|SALMON_QUANT' { conda = 'bioconda::salmon=1.10.3' //conda = 'bioconda::salmon=1.10.1' From 4e5d7a38d2c6fe355eaebde60611ec4c5b21f188 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 14:26:45 +0100 Subject: [PATCH 13/40] correct ucsc --- conf/arm.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 37a6d1211..933dfc928 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -128,8 +128,8 @@ process { } withName: 'UCSC_BEDGRAPHTOBIGWIG' { - conda = 'bioconda::ucsc-bedgraphtobigwig=445' - //conda = 'bioconda::ucsc-bedgraphtobigwig=469' + conda = 'bioconda::ucsc-bedgraphtobigwig=469' + //conda = 'bioconda::ucsc-bedgraphtobigwig=445' } withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { From 902367e6cb02990d70c1583bf52ec6ecb70f3b91 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 20:25:21 +0100 Subject: [PATCH 14/40] Triage arm deps --- conf/arm.config | 229 +++++++++++++++++++++++++----------------------- 1 file changed, 121 insertions(+), 108 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 933dfc928..4a6f22e53 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -1,144 +1,157 @@ process { + // // Apply software overrides for ARM compatibility - - withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { - conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' - //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' - } - - withName: 'STAR_GENOMEGENERATE_IGENOMES' { - conda = 'bioconda::star bioconda::samtools=1.21 conda-forge::gawk=5.1.0' - //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' - } - - withName: 'BBSPLIT' { - conda = 'bioconda::bbmap' - // conda = 'bioconda::bbmap=39.01' - } - - withName: 'CAT_FASTQ' { - conda = 'conda-forge::coreutils' - //conda = 'conda-forge::coreutils=8.30' - } - - withName: 'CAT_ADDITIONAL_FASTA' { - conda = 'conda-forge::python' - //conda = 'conda-forge::coreutils=3.9.5' - } - + // + + //// Tested, working, module updates in progress on main dev branch + withName: 'CUSTOM_GETCHROMSIZES' { conda = 'bioconda::samtools=1.21' //conda = 'bioconda::samtools=1.20 bioconda::htslib=1.20' } - + withName: 'CUSTOM_TX2GENE' { conda = 'python=3.13.0' //conda = 'python=3.9.5' } - - withName: 'FASTP' { - conda = 'bioconda::fastp' - //conda = 'bioconda::fastp=0.23.4' - } - - withName: 'FQ_SUBSAMPLE' { - conda = 'bioconda::fq' - //conda = 'bioconda::fq=0.9.1' - } - - withName: 'GFFREAD' { - conda = 'bioconda::gffread' - //conda = 'bioconda::gffread=0.12.7' - } - - withName: 'GUNZIP' { - conda = 'conda-forge::sed' - //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' - } - - withName: 'HISAT2_ALIGN' { - conda = 'bioconda::hisat2 bioconda::samtools' - //conda = 'bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1' - } - - withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { - conda = 'bioconda::hisat2' - //conda = 'bioconda::hisat2=2.2.1' - } - - withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { - conda = 'bioconda::kallisto' - //conda = 'bioconda::kallisto=0.48.0' - } - - withName: 'PICARD_MARKDUPLICATES' { - conda = 'bioconda::picard=3.3.0' - //conda = 'bioconda::picard=3.1.1' - } - - withName: 'PRESEQ_LCEXTRAP' { - conda = 'bioconda::preseq' - //conda = 'bioconda::preseq=3.1.2' - } - - withName: 'RSEM_CALCULATEEXPRESSION' { - conda = 'bioconda::rsem bioconda::star' - //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' - } - - withName: 'RSEM_PREPAREREFERENCE' { - conda = 'seqera::rsem seqera::star=2.6.1d' - //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' - } - + withName: 'SALMON_INDEX|SALMON_QUANT' { conda = 'bioconda::salmon=1.10.3' //conda = 'bioconda::salmon=1.10.1' } - + withName: 'SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_INDEX|SAMTOOLS_SORT|SAMTOOLS_STATS' { conda = 'bioconda::samtools=1.21 bioconda::htslib' //conda = 'bioconda::samtools=1.20 bioconda::htslib' } - - withName: 'SORTMERNA' { - conda = 'bioconda::sortmerna' - //conda = 'bioconda::sortmerna=4.3.6' - } - - withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { - conda = 'bioconda::star bioconda::samtools bioconda::htslib conda-forge::gawk' - //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' + + withName: 'TRIMGALORE' { + conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9' + //conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4' } - + withName: 'STRINGTIE_STRINGTIE' { conda = 'bioconda::stringtie=2.2.3' //conda = 'bioconda::stringtie=2.2.1' } - + withName: 'SUBREAD_FEATURECOUNTS' { conda = 'bioconda::subread=2.0.6' //conda = 'bioconda::subread=2.0.1' } - - withName: 'TRIMGALORE' { - conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9' - //conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4' - } withName: 'UCSC_BEDGRAPHTOBIGWIG' { conda = 'bioconda::ucsc-bedgraphtobigwig=469' //conda = 'bioconda::ucsc-bedgraphtobigwig=445' } - - withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { - conda = 'bioconda::umi_tools' - //conda = 'bioconda::umi_tools=1.1.5' + + //// Untested, but have aarch conda builds in bioconda/ conda-forge channels. + //// Should update the nf-core modules + + withName: 'BBSPLIT' { + conda = 'bioconda::bbmap=39.10' + // conda = 'bioconda::bbmap=39.01' + } + + withName: 'CAT_FASTQ' { + conda = 'conda-forge::coreutils=9.5' + //conda = 'conda-forge::coreutils=8.30' + } + + withName: 'CAT_ADDITIONAL_FASTA' { + conda = 'python=3.13.0' + //conda = 'conda-forge::coreutils=3.9.5' + } + + withName: 'FQ_SUBSAMPLE' { + conda = 'bioconda::fq=0.12.0' + //conda = 'bioconda::fq=0.9.1' } + + withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { + conda = 'bioconda::kallisto=0.51.1' + //conda = 'bioconda::kallisto=0.48.0' + } + + withName: 'PRESEQ_LCEXTRAP' { + conda = 'bioconda::preseq=3.2.0' + //conda = 'bioconda::preseq=3.1.2' + } + + withName: 'SORTMERNA' { + conda = 'bioconda::sortmerna=4.3.7' + //conda = 'bioconda::sortmerna=4.3.6' + } + + //// No longer necessary- dev branch version has an aarch 64 build (s) + + //withName: 'GUNZIP' { + // conda = 'conda-forge::sed' + // //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' + //} + + //withName: 'UNTAR' { + // conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' + // //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' + //} + + //withName: 'FASTP' { + // conda = 'bioconda::fastp' + // //conda = 'bioconda::fastp=0.23.4' + //} + + //withName: 'GFFREAD' { + // conda = 'bioconda::gffread' + // //conda = 'bioconda::gffread=0.12.7' + //} + + //withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { + // conda = 'bioconda::umi_tools' + // //conda = 'bioconda::umi_tools=1.1.5' + //} + + //// No aarch64 builds in bioconda / conda-forge channels + + //// a) have seqera aarch64 conda builds - withName: 'UNTAR' { - conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' - //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' + withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { + conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' + //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' + } + + withName: 'STAR_GENOMEGENERATE_IGENOMES' { + conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' + //conda = 'bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' } -} + + withName: 'RSEM_PREPAREREFERENCE' { + conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d' + //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' + } + + withName: 'RSEM_CALCULATEEXPRESSION' { + conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d' + //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' + } + + // NOTE THE OLDER STAR VERSION HERE! + + withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { + conda = 'seqera::star2.6.1d bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0' + //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' + } + + //// b) need aarch64 conda builds + + //withName: 'HISAT2_ALIGN' { + // conda = 'bioconda::hisat2 bioconda::samtools' + // //conda = 'bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1' + //} + + //withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { + // conda = 'bioconda::hisat2' + // //conda = 'bioconda::hisat2=2.2.1' + //} + +} From 328d02d1bd2c80c55743d804bc6e13db207fd66b Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 20:32:03 +0100 Subject: [PATCH 15/40] Non-igenomes STAR can use the latest star --- conf/arm.config | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 4a6f22e53..801473fa6 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -83,6 +83,11 @@ process { conda = 'bioconda::sortmerna=4.3.7' //conda = 'bioconda::sortmerna=4.3.6' } + + withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { + conda = 'seqera::star2.7.11b bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0' + //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' + } //// No longer necessary- dev branch version has an aarch 64 build (s) @@ -137,11 +142,6 @@ process { // NOTE THE OLDER STAR VERSION HERE! - withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { - conda = 'seqera::star2.6.1d bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0' - //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' - } - //// b) need aarch64 conda builds //withName: 'HISAT2_ALIGN' { From 2f92bfc2199e93ac8747128726130a09cb331544 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 20:44:00 +0100 Subject: [PATCH 16/40] remove rogue comment --- conf/arm.config | 2 -- 1 file changed, 2 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 801473fa6..55547a6fe 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -140,8 +140,6 @@ process { //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' } - // NOTE THE OLDER STAR VERSION HERE! - //// b) need aarch64 conda builds //withName: 'HISAT2_ALIGN' { From 0a563dcedf654ac152ae04e8f4f10f97a5251335 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 11:58:41 +0100 Subject: [PATCH 17/40] update arm conf --- conf/arm.config | 73 ++++++++++++++++++------------------------------- 1 file changed, 26 insertions(+), 47 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 55547a6fe..4a56788fe 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -45,25 +45,12 @@ process { conda = 'bioconda::ucsc-bedgraphtobigwig=469' //conda = 'bioconda::ucsc-bedgraphtobigwig=445' } - - //// Untested, but have aarch conda builds in bioconda/ conda-forge channels. - //// Should update the nf-core modules - + withName: 'BBSPLIT' { conda = 'bioconda::bbmap=39.10' // conda = 'bioconda::bbmap=39.01' } - withName: 'CAT_FASTQ' { - conda = 'conda-forge::coreutils=9.5' - //conda = 'conda-forge::coreutils=8.30' - } - - withName: 'CAT_ADDITIONAL_FASTA' { - conda = 'python=3.13.0' - //conda = 'conda-forge::coreutils=3.9.5' - } - withName: 'FQ_SUBSAMPLE' { conda = 'bioconda::fq=0.12.0' //conda = 'bioconda::fq=0.9.1' @@ -73,48 +60,32 @@ process { conda = 'bioconda::kallisto=0.51.1' //conda = 'bioconda::kallisto=0.48.0' } - + withName: 'PRESEQ_LCEXTRAP' { conda = 'bioconda::preseq=3.2.0' //conda = 'bioconda::preseq=3.1.2' } - - withName: 'SORTMERNA' { - conda = 'bioconda::sortmerna=4.3.7' - //conda = 'bioconda::sortmerna=4.3.6' - } - withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { - conda = 'seqera::star2.7.11b bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0' - //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' + withName: 'CAT_ADDITIONAL_FASTA' { + conda = 'python=3.13.0' + //conda = 'conda-forge::coreutils=3.9.5' } - //// No longer necessary- dev branch version has an aarch 64 build (s) - - //withName: 'GUNZIP' { - // conda = 'conda-forge::sed' - // //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' - //} - - //withName: 'UNTAR' { - // conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' - // //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' - //} - - //withName: 'FASTP' { - // conda = 'bioconda::fastp' - // //conda = 'bioconda::fastp=0.23.4' - //} + //// Proposed to nf-core with Seqera container + + // Seqera container, since coreutils in existing image (ubuntu) wouldn't + // match update + withName: 'CAT_FASTQ' { + conda = 'conda-forge::coreutils=9.5' + //conda = 'conda-forge::coreutils=8.30' + } - //withName: 'GFFREAD' { - // conda = 'bioconda::gffread' - // //conda = 'bioconda::gffread=0.12.7' - //} + // Seqera container to avoid updating a mulled container - //withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { - // conda = 'bioconda::umi_tools' - // //conda = 'bioconda::umi_tools=1.1.5' - //} + withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { + conda = 'bioconda::star2.7.11b bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0' + //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' + } //// No aarch64 builds in bioconda / conda-forge channels @@ -152,4 +123,12 @@ process { // //conda = 'bioconda::hisat2=2.2.1' //} + //// c) have aarch64 builds in bioconda, but with problems + // sortmerna gives 'illegal instruction' errors at 5.3.7 with either + // Biocontainers or Seqera Containers + withName: 'SORTMERNA' { + conda = 'bioconda::sortmerna=4.3.7' + //conda = 'bioconda::sortmerna=4.3.6' + } + } From 0be2d6a53fb70c2f8afc7ce55debdea68eb30b6e Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 14:02:56 +0100 Subject: [PATCH 18/40] Cut out module redundant software overrides --- conf/arm.config | 95 ------------------------------------------------- 1 file changed, 95 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 4a56788fe..cfcd283fa 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -1,92 +1,5 @@ process { - // - // Apply software overrides for ARM compatibility - // - - //// Tested, working, module updates in progress on main dev branch - - withName: 'CUSTOM_GETCHROMSIZES' { - conda = 'bioconda::samtools=1.21' - //conda = 'bioconda::samtools=1.20 bioconda::htslib=1.20' - } - - withName: 'CUSTOM_TX2GENE' { - conda = 'python=3.13.0' - //conda = 'python=3.9.5' - } - - withName: 'SALMON_INDEX|SALMON_QUANT' { - conda = 'bioconda::salmon=1.10.3' - //conda = 'bioconda::salmon=1.10.1' - } - - withName: 'SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_INDEX|SAMTOOLS_SORT|SAMTOOLS_STATS' { - conda = 'bioconda::samtools=1.21 bioconda::htslib' - //conda = 'bioconda::samtools=1.20 bioconda::htslib' - } - - withName: 'TRIMGALORE' { - conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9' - //conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4' - } - - withName: 'STRINGTIE_STRINGTIE' { - conda = 'bioconda::stringtie=2.2.3' - //conda = 'bioconda::stringtie=2.2.1' - } - - withName: 'SUBREAD_FEATURECOUNTS' { - conda = 'bioconda::subread=2.0.6' - //conda = 'bioconda::subread=2.0.1' - } - - withName: 'UCSC_BEDGRAPHTOBIGWIG' { - conda = 'bioconda::ucsc-bedgraphtobigwig=469' - //conda = 'bioconda::ucsc-bedgraphtobigwig=445' - } - - withName: 'BBSPLIT' { - conda = 'bioconda::bbmap=39.10' - // conda = 'bioconda::bbmap=39.01' - } - - withName: 'FQ_SUBSAMPLE' { - conda = 'bioconda::fq=0.12.0' - //conda = 'bioconda::fq=0.9.1' - } - - withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { - conda = 'bioconda::kallisto=0.51.1' - //conda = 'bioconda::kallisto=0.48.0' - } - - withName: 'PRESEQ_LCEXTRAP' { - conda = 'bioconda::preseq=3.2.0' - //conda = 'bioconda::preseq=3.1.2' - } - - withName: 'CAT_ADDITIONAL_FASTA' { - conda = 'python=3.13.0' - //conda = 'conda-forge::coreutils=3.9.5' - } - - //// Proposed to nf-core with Seqera container - - // Seqera container, since coreutils in existing image (ubuntu) wouldn't - // match update - withName: 'CAT_FASTQ' { - conda = 'conda-forge::coreutils=9.5' - //conda = 'conda-forge::coreutils=8.30' - } - - // Seqera container to avoid updating a mulled container - - withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { - conda = 'bioconda::star2.7.11b bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0' - //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' - } - //// No aarch64 builds in bioconda / conda-forge channels //// a) have seqera aarch64 conda builds @@ -123,12 +36,4 @@ process { // //conda = 'bioconda::hisat2=2.2.1' //} - //// c) have aarch64 builds in bioconda, but with problems - // sortmerna gives 'illegal instruction' errors at 5.3.7 with either - // Biocontainers or Seqera Containers - withName: 'SORTMERNA' { - conda = 'bioconda::sortmerna=4.3.7' - //conda = 'bioconda::sortmerna=4.3.6' - } - } From ed026be0c3bd823b1f01060c06180e8db39c0d24 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 17:42:03 +0100 Subject: [PATCH 19/40] Add frozen ARM builds --- conf/arm.config | 212 +++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 211 insertions(+), 1 deletion(-) diff --git a/conf/arm.config b/conf/arm.config index cfcd283fa..c8d3c379f 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -1,9 +1,219 @@ process { + //// Frozen ARM buids from Wave + + withName: GTF_FILTER { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f012a4fe624e7965c4c52fe1eb1b591a3d97cee5c16c5c0d654aa86ee1c0c801/data' : 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } + } + + withName: PREPROCESS_TRANSCRIPTS_FASTA_GENCODE { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4a/4ad78019c37ff4ab22c0dff6ab1af655c6438562ef644d0323861a97971d7694/data' : 'community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } + } + + withName: DESEQ2_QC { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/70/70a3d17733d2c21cff464c31a7a57438cea528bea84c675b7c474eaa7f075f57/data' : 'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:8bd3e9db55b129d7' } + } + + withName: GTF2BED { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/89/896a3e55b2f664def0f8707420e1f53b4c447adb99fd6a1432a155c3403b9199/data' : 'community.wave.seqera.io/library/perl:5.26.2--2a6adf51d600e047' } + } + + withName: MULTIQC_CUSTOM_BIOTYPE { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f012a4fe624e7965c4c52fe1eb1b591a3d97cee5c16c5c0d654aa86ee1c0c801/data' : 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } + } + + withName: RSEM_MERGE_COUNTS { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4a/4ad78019c37ff4ab22c0dff6ab1af655c6438562ef644d0323861a97971d7694/data' : 'community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } + } + + withName: UCSC_BEDCLIP { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5f/5f559cabdfda8b2937c4213d3a53547eb882b2fc8cc36ebfeff07481fa47823a/data' : 'community.wave.seqera.io/library/ucsc-bedclip:377--489576e83f1992e0' } + } + + withName: UCSC_BEDGRAPHTOBIGWIG { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/38/389312a4a6022c5f5d2510dfa9bedb0491b36c8a27e8d842c05de00bc3b5be76/data' : 'community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--1db18e1b19f8e5f1' } + } + + withName: CAT_FASTQ { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/38/38d3638640600b355110f9bca56c514e3cc068bf96b8b68f98cba2a59a053505/data' : 'community.wave.seqera.io/library/coreutils:9.5--3931e2d27d9884e5' } + } + + withName: RSEQC_TIN { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: RSEQC_READDISTRIBUTION { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: RSEQC_JUNCTIONSATURATION { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: RSEQC_READDUPLICATION { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: RSEQC_INFEREXPERIMENT { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: RSEQC_BAMSTAT { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: RSEQC_INNERDISTANCE { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: RSEQC_JUNCTIONANNOTATION { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: PICARD_MARKDUPLICATES { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c0/c0d4bbb10417a70d137a28da09329d9f9fbdf964a1cfeda24b05b618cae6b16f/data' : 'community.wave.seqera.io/library/picard:3.1.1--c28da730a329ab3c' } + } + + withName: QUALIMAP_RNASEQ { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7a/7aa0998788d327c6e7104c2c1e7bea2e8bb8fb7076ec5de3fdab4027e501b9a9/data' : 'community.wave.seqera.io/library/qualimap:2.3--8375b60bba97a2a6' } + } + + withName: SUBREAD_FEATURECOUNTS { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2a/2a81571bc8c4ac812adb76c51045a245041d7cc8923a2d7cc34a866588fead0c/data' : 'community.wave.seqera.io/library/subread:2.0.6--df9c6b502b57bb9c' } + } + + withName: MULTIQC { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6e/6e97dcafc5915f90f863e70153f96bbe47963ebfd08383454d8bcd7263696e4e/data' : 'community.wave.seqera.io/library/multiqc:1.25.1--4062a515975cacba' } + } + + withName: STRINGTIE_STRINGTIE { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9ebc6b1a27262420a5739330d369086b0d8c941a43b81d3fd0f741045bb3d46f/data' : 'community.wave.seqera.io/library/stringtie:2.2.3--77d8df3265c94ba1' } + } + + withName: UNTAR { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } + } + + withName: FQ_SUBSAMPLE { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b0/b00189d4f7eed55199354a3dff8a9a535e1dfb3a2f4c97f5d0bf9e388105795e/data' : 'community.wave.seqera.io/library/fq:0.12.0--ad6857b304869ce9' } + } + + withName: DUPRADAR { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/10141f8fd43964316d04214a5f7d99a62e11cdbab5bd2fcd4f7c3c06eca9f2f6/data' : 'community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--f75495d6abf45328' } + } + + withName: SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a7/a7d1ef576617b9790973bc9d178c4ef136a52b6337260c536cff6cd68f103b45/data' : 'community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--859858039875a2a5' } + } + + withName: STAR_GENOMEGENERATE { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a2/a2d5226e4ce3dee8b29154c16a87d282d96c76e75b6678d032643902591586e2/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:1d1b7da208684cac' } + } + + withName: STAR_ALIGN { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a2/a2d5226e4ce3dee8b29154c16a87d282d96c76e75b6678d032643902591586e2/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:1d1b7da208684cac' } + } + + withName: TXIMETA_TXIMPORT { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f8/f89ab1fef6e38e572ad1844d06f6d3d334d2b19a70c9e5d87bfc862b88728c23/data' : 'community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--3b0ca8a1710e2b2b' } + } + + withName: SORTMERNA { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f1/f161ea3d4083b7d8fcbf8524cb5ab69f386b4e36b771bb5abf9ccf8ab29e9775/data' : 'community.wave.seqera.io/library/sortmerna:4.3.7--4cc83a7bffbaaa61' } + } + + withName: PRESEQ_LCEXTRAP { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5ab535d5b4c88dc4837cab00919d4d5ea66dd4d6dc837d841886bef72145f435/data' : 'community.wave.seqera.io/library/preseq:3.2.0--80c9d2ffee38d3ac' } + } + + withName: BEDTOOLS_GENOMECOV { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/519a920dacc643078823740486c40d30b9f555c493217d9f72db04901350e009/data' : 'community.wave.seqera.io/library/bedtools:2.31.1--efd79503b8c63422' } + } + + withName: BBMAP_BBSPLIT { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/63ca91c8bf7285296777de219e5d5a71d2a7de47599cbc94441aced7868a4f83/data' : 'community.wave.seqera.io/library/bbmap:39.10--908996c2fb304bec' } + } + + withName: FASTQC { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fd/fd39534bf298698cbe3ee4d4a6f1e73330ec4bca44c38dd9a4d06cb5ea838017/data' : 'community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a' } + } + + withName: KALLISTO_QUANT { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24655791b5db39ffdfffa8e5aeabfd11dda4553b5311ddb22e724c38b1591e8d/data' : 'community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } + } + + withName: KALLISTO_INDEX { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24655791b5db39ffdfffa8e5aeabfd11dda4553b5311ddb22e724c38b1591e8d/data' : 'community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } + } + + withName: SAMTOOLS_SORT { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } + } + + withName: SAMTOOLS_IDXSTATS { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } + } + + withName: SAMTOOLS_INDEX { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } + } + + withName: SAMTOOLS_FLAGSTAT { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } + } + + withName: SAMTOOLS_STATS { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } + } + + withName: CUSTOM_CATADDITIONALFASTA { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c1/c17acd739990ad12c06583f57b097014c2bde5a91d0977fd102864a82f95e136/data' : 'community.wave.seqera.io/library/python:3.12.2--0d47e6fe32e00784' } + } + + withName: CUSTOM_TX2GENE { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/60/6029f43341dc0bea31d14c2ce4c779d7a48dfed6ecb29ce1630b8378c560c490/data' : 'community.wave.seqera.io/library/python:3.10.4--d0dc5eb8ea72fa82' } + } + + withName: CUSTOM_GETCHROMSIZES { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } + } + + withName: UMITOOLS_PREPAREFORRSEM { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } + } + + withName: UMITOOLS_EXTRACT { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } + } + + withName: UMITOOLS_DEDUP { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } + } + + withName: GFFREAD { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9e6db95013607b07689e38ee37a654d029236de77fdfde97fe1866f45d01e064/data' : 'community.wave.seqera.io/library/gffread:0.12.7--1577aa7c95340d9f' } + } + + withName: FASTP { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7e/7ec6234f24305b9694b89de0352fff942ce1d68f840184020b0b9135bc54bda1/data' : 'community.wave.seqera.io/library/fastp:0.23.4--c1051f83dcae53f5' } + } + + withName: SALMON_QUANT { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b8/b8e3bcb1daa42497d0159cd5ae3b6d164b4470a972dd72d9d10b365fa166e5a4/data' : 'community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } + } + + withName: SALMON_INDEX { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b8/b8e3bcb1daa42497d0159cd5ae3b6d164b4470a972dd72d9d10b365fa166e5a4/data' : 'community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } + } + + withName: GUNZIP { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } + } + //// No aarch64 builds in bioconda / conda-forge channels //// a) have seqera aarch64 conda builds - + withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' From a8d514f79220ffd10a0cb6b7e0d6acd5714ef179 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 18:16:26 +0100 Subject: [PATCH 20/40] Container directives for conda overrides --- conf/arm.config | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index c8d3c379f..b80fe295c 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -215,23 +215,31 @@ process { //// a) have seqera aarch64 conda builds withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { - conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' + + conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/18/18b787cb710e54b55e04d8df4f5d363b3581c0f6008a908d7ab7de03275dfedb/data' : 'community.wave.seqera.io/library/star_samtools_gawk:c0246261b9d809e1' } } withName: 'STAR_GENOMEGENERATE_IGENOMES' { - conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' //conda = 'bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' + + conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/18/18b787cb710e54b55e04d8df4f5d363b3581c0f6008a908d7ab7de03275dfedb/data' : 'community.wave.seqera.io/library/star_samtools_gawk:c0246261b9d809e1' } } withName: 'RSEM_PREPAREREFERENCE' { - conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d' //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' + + conda = 'seqera::rsem=1.3.3 seqera::star=2.7.10a' + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } } withName: 'RSEM_CALCULATEEXPRESSION' { - conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d' //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' + + conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d' + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } } //// b) need aarch64 conda builds From 8e147116f934f6e31788307bd5a472d8032521f6 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 18:38:07 +0100 Subject: [PATCH 21/40] Temporary Trimgalore override, singularity fixes for rsem processes --- conf/arm.config | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index b80fe295c..ef488cc05 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -210,6 +210,18 @@ process { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } } + //// Remove this once we've got a new Biocontainer for trimgalore with the + //// newer cutadapt, and we've update the nf-core module + //// https://github.com/bioconda/bioconda-recipes/pull/51563 + + withName: TRIMGALORE { + //conda = 'bioconda::cutadapt=4.2 trim-galore=0.6.10' + + conda = 'bioconda::cutadapt=4.9 trim-galore=0.6.10' + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0d/0dda1e09d10d1e2994ea85843b1e3d62212598ca5047e0ab419d5d87db637057/data' : 'community.wave.seqera.io/library/cutadapt_trim-galore:1cd58fa242e634da' } + + } + //// No aarch64 builds in bioconda / conda-forge channels //// a) have seqera aarch64 conda builds @@ -232,14 +244,14 @@ process { //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' conda = 'seqera::rsem=1.3.3 seqera::star=2.7.10a' - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3/data' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } } withName: 'RSEM_CALCULATEEXPRESSION' { //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d' - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3/data' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } } //// b) need aarch64 conda builds From 161cf95412b8a7ae40ba34d499ae783c94e47b6d Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 18:49:37 +0100 Subject: [PATCH 22/40] update docs --- docs/usage.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/docs/usage.md b/docs/usage.md index ad2aa4e26..c9302fa1f 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -116,6 +116,10 @@ If you would like to reduce the number of reads used in the analysis, for exampl ## Alignment options +:::note +Not currently available using ARM architecture ('-profile arm') +::: + By default, the pipeline uses [STAR](https://github.com/alexdobin/STAR) (i.e. `--aligner star_salmon`) to map the raw FastQ reads to the reference genome, project the alignments onto the transcriptome and to perform the downstream BAM-level quantification with [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html). STAR is fast but requires a lot of memory to run, typically around 38GB for the Human GRCh37 reference genome. Since the [RSEM](https://github.com/deweylab/RSEM) (i.e. `--aligner star_rsem`) workflow in the pipeline also uses STAR you should use the [HISAT2](https://ccb.jhu.edu/software/hisat2/index.shtml) aligner (i.e. `--aligner hisat2`) if you have memory limitations. You also have the option to pseudoalign and quantify your data directly with [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html) or [Kallisto](https://pachterlab.github.io/kallisto/) by specifying `salmon` or `kallisto` to the `--pseudo_aligner` parameter. The selected pseudoaligner will then be run in addition to the standard alignment workflow defined by `--aligner`, mainly because it allows you to obtain QC metrics with respect to the genomic alignments. However, you can provide the `--skip_alignment` parameter if you would like to run Salmon or Kallisto in isolation. By default, the pipeline will use the genome fasta and gtf file to generate the transcripts fasta file, and then to build the Salmon index. You can override these parameters using the `--transcript_fasta` and `--salmon_index` parameters, respectively. @@ -298,6 +302,10 @@ By default, the input GTF file will be filtered to ensure that sequence names co ## Contamination screening options +:::note +Not currently available using ARM architecture ('-profile arm') +::: + The pipeline provides the option to scan unaligned reads for contamination from other species using [Kraken2](https://ccb.jhu.edu/software/kraken2/), with the possibility of applying corrections from [Bracken](https://ccb.jhu.edu/software/bracken/). Since running Bracken is not computationally expensive, we recommend always using it to refine the abundance estimates generated by Kraken2. It is important to note that the accuracy of Kraken2 is [highly dependent on the database](https://doi.org/10.1099/mgen.0.000949) used. Specifically, it is [crucial](https://doi.org/10.1128/mbio.01607-23) to ensure that the host genome is included in the database. If you are particularly concerned about certain contaminants, it may be beneficial to use a smaller, more focused database containing primarily those contaminants instead of the full standard database. Various pre-built databases [are available for download](https://benlangmead.github.io/aws-indexes/k2), and instructions for building a custom database can be found in the [Kraken2 documentation](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown). Additionally, genomes of contaminants detected in previous sequencing experiments are available on the [OpenContami website](https://openlooper.hgc.jp/opencontami/help/help_oct.php). @@ -420,6 +428,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later). - `conda` - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. + - A configuration profile that will set `docker.runOptions` appropriately for ARM architectures, and apply overrides supplying ARM-compatible containers and Conda environments. ### `-resume` From caad7fa623a0e88ad2a07cfd80493adc1032bd76 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 20:07:50 +0100 Subject: [PATCH 23/40] Fix argument conflict between STAR versions --- subworkflows/local/align_star/nextflow.config | 68 +++++++++++-------- 1 file changed, 40 insertions(+), 28 deletions(-) diff --git a/subworkflows/local/align_star/nextflow.config b/subworkflows/local/align_star/nextflow.config index 3d07c9e88..b676150dd 100644 --- a/subworkflows/local/align_star/nextflow.config +++ b/subworkflows/local/align_star/nextflow.config @@ -1,36 +1,48 @@ +def generateStarAlignArgs(save_unaligned, contaminant_screening, extra_star_align_args) { + def argsToMap = { String args -> + args.split(/\s(?=--)/).collectEntries { + def parts = it.trim().split(/\s+/, 2) + [(parts[0]): parts.size() > 1 ? parts[1] : ''] + } + } + + def base_args = """ + --quantMode TranscriptomeSAM + --twopassMode Basic + --outSAMtype BAM Unsorted + --readFilesCommand zcat + --runRNGseed 0 + --outFilterMultimapNmax 20 + --alignSJDBoverhangMin 1 + --outSAMattributes NH HI AS NM MD + --outSAMstrandField intronMotif + """.trim() + + if (save_unaligned || contaminant_screening) { + base_args += "\n--outReadsUnmapped Fastx" + } + + def final_args_map = argsToMap(base_args) + (extra_star_align_args ? argsToMap(extra_star_align_args) : [:]) + final_args_map.collect { key, value -> "${key} ${value}".trim() }.join(' ') +} + if (!params.skip_alignment && params.aligner == 'star_salmon') { process { - withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { - ext.args = { - // Function to convert argument strings into a map - def argsToMap = { String args -> - args.split("\\s(?=--)").collectEntries { - def parts = it.trim().split(/\s+/, 2) - [(parts.first()): parts.last()] - } - } - - // Initialize the map with preconfigured values - def preset_args_map = argsToMap(""" - --quantMode TranscriptomeSAM - --twopassMode Basic - --outSAMtype BAM Unsorted - --readFilesCommand zcat - --runRNGseed 0 - --outFilterMultimapNmax 20 - --alignSJDBoverhangMin 1 - --outSAMattributes NH HI AS NM MD - --quantTranscriptomeSAMoutput BanSingleEnd - --outSAMstrandField intronMotif - ${params.save_unaligned || params.contaminant_screening ? '--outReadsUnmapped Fastx' : ''} - """.trim()) - // Consolidate the extra arguments - def final_args_map = preset_args_map + (params.extra_star_align_args ? argsToMap(params.extra_star_align_args) : [:]) + // We have to condition this, because the args are slightly different between the latest STAR and the one compatible with iGenomes - // Convert the map back to a list and then to a single string - final_args_map.collect { key, value -> "${key} ${value}" }.join(' ').trim() + withName: '.*:ALIGN_STAR:STAR_ALIGN' { + ext.args = { + generateStarAlignArgs(params.save_unaligned, params.contaminant_screening, params.extra_star_align_args + ' --quantTranscriptomeSAMoutput BanSingleEnd') + } + } + withName: 'ALIGN_STAR:STAR_ALIGN_IGENOMES' { + ext.args = { + generateStarAlignArgs(params.save_unaligned, params.contaminant_screening, params.extra_star_align_args + ' --quantTranscriptomeBan Singleend') } + + } + withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { publishDir = [ [ From cdfb98b9dcb1512392c05af947bab2a637e21d12 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 19:50:23 +0000 Subject: [PATCH 24/40] Fix config error --- subworkflows/local/align_star/nextflow.config | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/subworkflows/local/align_star/nextflow.config b/subworkflows/local/align_star/nextflow.config index b676150dd..86960b2e1 100644 --- a/subworkflows/local/align_star/nextflow.config +++ b/subworkflows/local/align_star/nextflow.config @@ -36,11 +36,10 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') { generateStarAlignArgs(params.save_unaligned, params.contaminant_screening, params.extra_star_align_args + ' --quantTranscriptomeSAMoutput BanSingleEnd') } } - withName: 'ALIGN_STAR:STAR_ALIGN_IGENOMES' { + withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { ext.args = { generateStarAlignArgs(params.save_unaligned, params.contaminant_screening, params.extra_star_align_args + ' --quantTranscriptomeBan Singleend') } - } withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { From 524e19eacb6b80a72bb8460f3e4e6f5f096f2254 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 21:44:55 +0100 Subject: [PATCH 25/40] Correction to star rsem --- conf/arm.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/arm.config b/conf/arm.config index ef488cc05..3a2b63d9b 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -250,7 +250,7 @@ process { withName: 'RSEM_CALCULATEEXPRESSION' { //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' - conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d' + conda = 'seqera::rsem=1.3.3 seqera::star=2.7.10a' container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3/data' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } } From 4f8de9450eaa6ac691afb1cad146b271f3a5e760 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 22:17:41 +0100 Subject: [PATCH 26/40] Refine config setup --- subworkflows/local/align_star/nextflow.config | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/align_star/nextflow.config b/subworkflows/local/align_star/nextflow.config index 86960b2e1..106710e05 100644 --- a/subworkflows/local/align_star/nextflow.config +++ b/subworkflows/local/align_star/nextflow.config @@ -33,12 +33,20 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') { withName: '.*:ALIGN_STAR:STAR_ALIGN' { ext.args = { - generateStarAlignArgs(params.save_unaligned, params.contaminant_screening, params.extra_star_align_args + ' --quantTranscriptomeSAMoutput BanSingleEnd') + generateStarAlignArgs( + params.save_unaligned, + params.contaminant_screening, + (params.extra_star_align_args ?: '') + ' --quantTranscriptomeSAMoutput BanSingleEnd' + ) } } withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { ext.args = { - generateStarAlignArgs(params.save_unaligned, params.contaminant_screening, params.extra_star_align_args + ' --quantTranscriptomeBan Singleend') + generateStarAlignArgs( + params.save_unaligned, + params.contaminant_screening, + (params.extra_star_align_args ?: '') + ' --quantTranscriptomeBan Singleend' + ) } } withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { From a1d558e57e051453dfcd409fee20a4431d43b4f4 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 22:30:32 +0100 Subject: [PATCH 27/40] Bump trimgalore module --- modules.json | 4 +- modules/nf-core/trimgalore/environment.yml | 2 +- modules/nf-core/trimgalore/main.nf | 4 +- .../trimgalore/tests/main.nf.test.snap | 20 ++++---- .../tests/main.nf.test | 10 ++++ .../tests/main.nf.test.snap | 48 +++++++++---------- 6 files changed, 49 insertions(+), 39 deletions(-) diff --git a/modules.json b/modules.json index 7f889aeec..61692d607 100644 --- a/modules.json +++ b/modules.json @@ -245,7 +245,7 @@ }, "trimgalore": { "branch": "master", - "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", + "git_sha": "8c5eeedd45e295fc9a4f164631da6a8b37e6b9c6", "installed_by": ["fastq_fastqc_umitools_trimgalore"] }, "tximeta/tximport": { @@ -333,7 +333,7 @@ }, "fastq_fastqc_umitools_trimgalore": { "branch": "master", - "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", + "git_sha": "8c5eeedd45e295fc9a4f164631da6a8b37e6b9c6", "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] }, "fastq_qc_trim_filter_setstrandedness": { diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml index 910ffa882..622407eda 100644 --- a/modules/nf-core/trimgalore/environment.yml +++ b/modules/nf-core/trimgalore/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::cutadapt=4.2 + - bioconda::cutadapt=4.9 - bioconda::trim-galore=0.6.10 diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 30d17edc1..8a2fc54b3 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -4,8 +4,8 @@ process TRIMGALORE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.10--hdfd78af_0' : - 'biocontainers/trim-galore:0.6.10--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/trim-galore%3A0.6.10--hdfd78af_1' : + 'biocontainers/trim-galore:0.6.10--hdfd78af_1' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap index 61b3504a9..21da84933 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test.snap +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "test_trimgalore_single_end": { "content": [ [ - "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:50:36.440264431" + "timestamp": "2024-10-22T19:23:17.969056957" }, "test_trimgalore_single_end - stub": { "content": [ @@ -42,7 +42,7 @@ ], "5": [ - "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ], "html": [ @@ -69,7 +69,7 @@ ], "versions": [ - "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ], "zip": [ @@ -80,7 +80,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:50:51.25902234" + "timestamp": "2024-10-22T19:23:28.617831159" }, "test_trimgalore_paired_end - stub": { "content": [ @@ -119,7 +119,7 @@ ], "5": [ - "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ], "html": [ @@ -152,7 +152,7 @@ ], "versions": [ - "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ], "zip": [ @@ -163,18 +163,18 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:51:19.024228479" + "timestamp": "2024-10-22T19:23:51.539787731" }, "test_trimgalore_paired_end": { "content": [ [ - "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:51:02.471703095" + "timestamp": "2024-10-22T19:23:41.16485915" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test index 1043d06ad..96e05765b 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test @@ -5,6 +5,16 @@ nextflow_workflow { workflow "FASTQ_FASTQC_UMITOOLS_TRIMGALORE" config './nextflow.config' + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/fastq_fastqc_umitools_trimgalore" + tag "fastqc" + tag "umitools/extract" + tag "trimgalore" + + tag "FASTQC" + tag "UMITOOLS_EXTRACT" + tag "TRIMGALORE" test("test single end read with UMI") { diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap index f8a746aa6..834aaa931 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap @@ -61,8 +61,8 @@ ], "9": [ "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", - "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ], "fastqc_html": [ [ @@ -123,8 +123,8 @@ ], "versions": [ "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", - "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ] } ], @@ -132,7 +132,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:18:56.222595833" + "timestamp": "2024-10-22T19:25:19.153139356" }, "test paired end read without UMI - stub": { "content": [ @@ -192,8 +192,8 @@ ] ], "9": [ - "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ], "fastqc_html": [ [ @@ -250,8 +250,8 @@ ], "versions": [ - "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ] } ], @@ -259,7 +259,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:19:07.775855857" + "timestamp": "2024-10-22T19:25:30.433084765" }, "test paired end read without UMI": { "content": [ @@ -288,15 +288,15 @@ ], [ - "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:18:19.621101515" + "timestamp": "2024-10-22T19:24:40.341840093" }, "test single end read with UMI": { "content": [ @@ -323,15 +323,15 @@ ], [ "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", - "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:17:51.049984482" + "timestamp": "2024-10-22T19:24:09.307037853" }, "test paired end read with UMI": { "content": [ @@ -358,15 +358,15 @@ ], [ "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", - "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:18:07.106739839" + "timestamp": "2024-10-22T19:24:26.93011239" }, "test skip all steps": { "content": [ @@ -448,8 +448,8 @@ ], "9": [ "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", - "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ], "fastqc_html": [ [ @@ -510,8 +510,8 @@ ], "versions": [ "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", - "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ] } ], @@ -519,6 +519,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:18:42.513733457" + "timestamp": "2024-10-22T19:25:05.585472049" } } \ No newline at end of file From dae2899782f635e89450a3c2ad87d5348224b5c3 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 22:38:34 +0100 Subject: [PATCH 28/40] Fix up ARM profile for updated trim-galore --- conf/arm.config | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 3a2b63d9b..322a239e7 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -210,15 +210,8 @@ process { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } } - //// Remove this once we've got a new Biocontainer for trimgalore with the - //// newer cutadapt, and we've update the nf-core module - //// https://github.com/bioconda/bioconda-recipes/pull/51563 - withName: TRIMGALORE { - //conda = 'bioconda::cutadapt=4.2 trim-galore=0.6.10' - - conda = 'bioconda::cutadapt=4.9 trim-galore=0.6.10' - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0d/0dda1e09d10d1e2994ea85843b1e3d62212598ca5047e0ab419d5d87db637057/data' : 'community.wave.seqera.io/library/cutadapt_trim-galore:1cd58fa242e634da' } + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/10e7b91ef06bdf5790120809afc8cf36aac0261b618d810c952d5afd60dd5ed2/data' : 'community.wave.seqera.io/library/cutadapt_trim-galore:2aa2fc797328573b' } } From d3580a4bc96d74b623dfecddff73ad4c08b7e7ec Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 10:38:26 +0100 Subject: [PATCH 29/40] Apply suggestions from code review Co-authored-by: Harshil Patel --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index c9302fa1f..1e3261e90 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -117,7 +117,7 @@ If you would like to reduce the number of reads used in the analysis, for exampl ## Alignment options :::note -Not currently available using ARM architecture ('-profile arm') +The `--aligner hisat2` option is not currently supported using ARM architecture ('-profile arm') ::: By default, the pipeline uses [STAR](https://github.com/alexdobin/STAR) (i.e. `--aligner star_salmon`) to map the raw FastQ reads to the reference genome, project the alignments onto the transcriptome and to perform the downstream BAM-level quantification with [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html). STAR is fast but requires a lot of memory to run, typically around 38GB for the Human GRCh37 reference genome. Since the [RSEM](https://github.com/deweylab/RSEM) (i.e. `--aligner star_rsem`) workflow in the pipeline also uses STAR you should use the [HISAT2](https://ccb.jhu.edu/software/hisat2/index.shtml) aligner (i.e. `--aligner hisat2`) if you have memory limitations. From 32f7d3245b2a73f3ca0b87387723070f08017e90 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 10:42:54 +0100 Subject: [PATCH 30/40] Apply suggestions from code review Co-authored-by: Harshil Patel --- conf/arm.config | 15 +++++++++------ modules/nf-core/trimgalore/main.nf | 2 +- .../tests/main.nf.test | 10 ---------- 3 files changed, 10 insertions(+), 17 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 322a239e7..ad4fb2eb9 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -1,6 +1,8 @@ process { - //// Frozen ARM buids from Wave + // + // Tools that have native Conda builds for AMD and ARM + // withName: GTF_FILTER { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f012a4fe624e7965c4c52fe1eb1b591a3d97cee5c16c5c0d654aa86ee1c0c801/data' : 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } @@ -215,13 +217,12 @@ process { } - //// No aarch64 builds in bioconda / conda-forge channels + // + // Tools that do not have native Conda builds for AMD and ARM. Required custom builds in seqera Conda channel. + // - //// a) have seqera aarch64 conda builds withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { - //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' - conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/18/18b787cb710e54b55e04d8df4f5d363b3581c0f6008a908d7ab7de03275dfedb/data' : 'community.wave.seqera.io/library/star_samtools_gawk:c0246261b9d809e1' } } @@ -247,7 +248,9 @@ process { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3/data' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } } - //// b) need aarch64 conda builds + // + // Tools currently unsupported for ARM + // //withName: 'HISAT2_ALIGN' { // conda = 'bioconda::hisat2 bioconda::samtools' diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 8a2fc54b3..02f4b16ad 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -4,7 +4,7 @@ process TRIMGALORE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/trim-galore%3A0.6.10--hdfd78af_1' : + 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.10--hdfd78af_1' : 'biocontainers/trim-galore:0.6.10--hdfd78af_1' }" input: diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test index 96e05765b..1043d06ad 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test @@ -5,16 +5,6 @@ nextflow_workflow { workflow "FASTQ_FASTQC_UMITOOLS_TRIMGALORE" config './nextflow.config' - tag "subworkflows" - tag "subworkflows_nfcore" - tag "subworkflows/fastq_fastqc_umitools_trimgalore" - tag "fastqc" - tag "umitools/extract" - tag "trimgalore" - - tag "FASTQC" - tag "UMITOOLS_EXTRACT" - tag "TRIMGALORE" test("test single end read with UMI") { From 7df162fcb3f50f4a1e3d91025cb45a9784214f1b Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 10:47:57 +0100 Subject: [PATCH 31/40] Add notes for kraken2/ braken --- conf/arm.config | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/conf/arm.config b/conf/arm.config index ad4fb2eb9..b01e09465 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -262,4 +262,10 @@ process { // //conda = 'bioconda::hisat2=2.2.1' //} -} + // withName: 'KRAKEN2_KRAKEN2' { + // conda = 'bioconda::kraken2=2.1.3 coreutils=9.4 pigz=2.8' + //} + + // withName: 'BRACKEN_BRACKEN' { + // conda = 'bioconda::bracken=2.9' + //} From 642d2a869d76322711941850fd54a53c2097f43a Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 11:07:55 +0100 Subject: [PATCH 32/40] Update docs --- docs/usage.md | 27 ++++++++++++++++++++++++++- 1 file changed, 26 insertions(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index 1e3261e90..26be822fd 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -303,7 +303,7 @@ By default, the input GTF file will be filtered to ensure that sequence names co ## Contamination screening options :::note -Not currently available using ARM architecture ('-profile arm') +The `--contaminant_screening` option is not currently available using ARM architecture ('-profile arm') ::: The pipeline provides the option to scan unaligned reads for contamination from other species using [Kraken2](https://ccb.jhu.edu/software/kraken2/), with the possibility of applying corrections from [Bracken](https://ccb.jhu.edu/software/bracken/). Since running Bracken is not computationally expensive, we recommend always using it to refine the abundance estimates generated by Kraken2. @@ -364,6 +364,26 @@ genome: 'GRCh37' You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). +### Running on Linux ARM architectures + +The pipeline can be executed in an ARM compatible mode by specifying the ARM profile, for example: + +```bash +nextflow run \ + nf-core/rnaseq \ + --input \ + --outdir \ + --gtf \ + --fasta \ + -profile docker,arm +``` + +This will use ARM-compatible containers, and apply a small number of overrides to Conda definitions to support ARM operation. + +:::warning +Please note that the ARM profile is experimental. It is expected to function correctly in all cases unless explicitly indicated otherwise—currently, exceptions include the use of the hisat2 aligner and contaminant screening via kraken2. However, because testing is presently conducted manually, we cannot guarantee its reliability. +::: + ### Updating the pipeline When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: @@ -428,8 +448,13 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later). - `conda` - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. +- `arm` - A configuration profile that will set `docker.runOptions` appropriately for ARM architectures, and apply overrides supplying ARM-compatible containers and Conda environments. +:::warning +Please note that the ARM profile is experimental. It is expected to function correctly in all cases unless explicitly indicated otherwise—currently, exceptions include the use of the hisat2 aligner and contaminant screening via kraken2. However, because testing is presently conducted manually, we cannot guarantee its reliability. +::: + ### `-resume` Specify this when restarting a pipeline. Nextflow will use cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously. For input to be considered the same, not only the names must be identical but the files' contents as well. For more info about this parameter, see [this blog post](https://www.nextflow.io/blog/2019/demystifying-nextflow-resume.html). From d9e534da8860a5b07c3f3577fcc5248f74d60f41 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 11:08:52 +0100 Subject: [PATCH 33/40] prettier --- docs/usage.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 26be822fd..581ed9598 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -366,7 +366,7 @@ You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-c ### Running on Linux ARM architectures -The pipeline can be executed in an ARM compatible mode by specifying the ARM profile, for example: +The pipeline can be executed in an ARM compatible mode by specifying the ARM profile, for example: ```bash nextflow run \ @@ -378,7 +378,7 @@ nextflow run \ -profile docker,arm ``` -This will use ARM-compatible containers, and apply a small number of overrides to Conda definitions to support ARM operation. +This will use ARM-compatible containers, and apply a small number of overrides to Conda definitions to support ARM operation. :::warning Please note that the ARM profile is experimental. It is expected to function correctly in all cases unless explicitly indicated otherwise—currently, exceptions include the use of the hisat2 aligner and contaminant screening via kraken2. However, because testing is presently conducted manually, we cannot guarantee its reliability. From d4fcb5602f06e41ed204d5536c143dfc2ba0a8f5 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 11:11:31 +0100 Subject: [PATCH 34/40] lint fix --- conf/arm.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/arm.config b/conf/arm.config index b01e09465..c28d97099 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -265,7 +265,7 @@ process { // withName: 'KRAKEN2_KRAKEN2' { // conda = 'bioconda::kraken2=2.1.3 coreutils=9.4 pigz=2.8' //} - + // withName: 'BRACKEN_BRACKEN' { // conda = 'bioconda::bracken=2.9' //} From 896dd74cf8a669714ee829f5ff355f32a6f52ecd Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 10:36:47 +0000 Subject: [PATCH 35/40] [skip ci] Reorg ARM bits --- docs/usage.md | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 581ed9598..851e20c7d 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -366,6 +366,10 @@ You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-c ### Running on Linux ARM architectures +:::warning +Please note that the ARM profile is experimental. It is expected to function correctly in all cases unless explicitly indicated otherwise—currently, exceptions include the use of the hisat2 aligner and contaminant screening via kraken2. However, because testing is presently conducted manually, we cannot guarantee its reliability. +::: + The pipeline can be executed in an ARM compatible mode by specifying the ARM profile, for example: ```bash @@ -378,11 +382,7 @@ nextflow run \ -profile docker,arm ``` -This will use ARM-compatible containers, and apply a small number of overrides to Conda definitions to support ARM operation. - -:::warning -Please note that the ARM profile is experimental. It is expected to function correctly in all cases unless explicitly indicated otherwise—currently, exceptions include the use of the hisat2 aligner and contaminant screening via kraken2. However, because testing is presently conducted manually, we cannot guarantee its reliability. -::: +This will use ARM-compatible containers, and apply a small number of overrides to Conda definitions to support ARM operations. ### Updating the pipeline @@ -449,11 +449,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - `conda` - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. - `arm` - - A configuration profile that will set `docker.runOptions` appropriately for ARM architectures, and apply overrides supplying ARM-compatible containers and Conda environments. - -:::warning -Please note that the ARM profile is experimental. It is expected to function correctly in all cases unless explicitly indicated otherwise—currently, exceptions include the use of the hisat2 aligner and contaminant screening via kraken2. However, because testing is presently conducted manually, we cannot guarantee its reliability. -::: + - A configuration profile that will set `docker.runOptions` appropriately for ARM architectures, and apply overrides supplying ARM-compatible containers and Conda environments. See [Running on Linux ARM architectures](#running-on-linux-arm-architectures). ### `-resume` From 314ea855fcc6bb55546adffb9f880280c917a68e Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 23 Oct 2024 12:37:19 +0200 Subject: [PATCH 36/40] Update arm.config --- conf/arm.config | 134 ++++++++++++++++++++++++------------------------ 1 file changed, 68 insertions(+), 66 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index c28d97099..5169bbc6a 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -1,249 +1,253 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running the pipeline with ARM architecture +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines custom containers and Conda definitions required to run pipeline with ARM. + + Use as follows: + nextflow run nf-core/rnaseq -profile ,arm + +---------------------------------------------------------------------------------------- +*/ + process { // // Tools that have native Conda builds for AMD and ARM // - withName: GTF_FILTER { + withName: 'GTF_FILTER' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f012a4fe624e7965c4c52fe1eb1b591a3d97cee5c16c5c0d654aa86ee1c0c801/data' : 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } } - withName: PREPROCESS_TRANSCRIPTS_FASTA_GENCODE { + withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4a/4ad78019c37ff4ab22c0dff6ab1af655c6438562ef644d0323861a97971d7694/data' : 'community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } } - withName: DESEQ2_QC { + withName: 'DESEQ2_QC' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/70/70a3d17733d2c21cff464c31a7a57438cea528bea84c675b7c474eaa7f075f57/data' : 'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:8bd3e9db55b129d7' } } - withName: GTF2BED { + withName: 'GTF2BED' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/89/896a3e55b2f664def0f8707420e1f53b4c447adb99fd6a1432a155c3403b9199/data' : 'community.wave.seqera.io/library/perl:5.26.2--2a6adf51d600e047' } } - withName: MULTIQC_CUSTOM_BIOTYPE { + withName: 'MULTIQC_CUSTOM_BIOTYPE' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f012a4fe624e7965c4c52fe1eb1b591a3d97cee5c16c5c0d654aa86ee1c0c801/data' : 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } } - withName: RSEM_MERGE_COUNTS { + withName: 'RSEM_MERGE_COUNTS' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4a/4ad78019c37ff4ab22c0dff6ab1af655c6438562ef644d0323861a97971d7694/data' : 'community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } } - withName: UCSC_BEDCLIP { + withName: 'UCSC_BEDCLIP' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5f/5f559cabdfda8b2937c4213d3a53547eb882b2fc8cc36ebfeff07481fa47823a/data' : 'community.wave.seqera.io/library/ucsc-bedclip:377--489576e83f1992e0' } } - withName: UCSC_BEDGRAPHTOBIGWIG { + withName: 'UCSC_BEDGRAPHTOBIGWIG' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/38/389312a4a6022c5f5d2510dfa9bedb0491b36c8a27e8d842c05de00bc3b5be76/data' : 'community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--1db18e1b19f8e5f1' } } - withName: CAT_FASTQ { + withName: 'CAT_FASTQ' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/38/38d3638640600b355110f9bca56c514e3cc068bf96b8b68f98cba2a59a053505/data' : 'community.wave.seqera.io/library/coreutils:9.5--3931e2d27d9884e5' } } - withName: RSEQC_TIN { + withName: 'RSEQC_TIN' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } - withName: RSEQC_READDISTRIBUTION { + withName: 'RSEQC_READDISTRIBUTION' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } - withName: RSEQC_JUNCTIONSATURATION { + withName: 'RSEQC_JUNCTIONSATURATION' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } - withName: RSEQC_READDUPLICATION { + withName: 'RSEQC_READDUPLICATION' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } - withName: RSEQC_INFEREXPERIMENT { + withName: 'RSEQC_INFEREXPERIMENT' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } - withName: RSEQC_BAMSTAT { + withName: 'RSEQC_BAMSTAT' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } - withName: RSEQC_INNERDISTANCE { + withName: 'RSEQC_INNERDISTANCE' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } - withName: RSEQC_JUNCTIONANNOTATION { + withName: 'RSEQC_JUNCTIONANNOTATION' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } - withName: PICARD_MARKDUPLICATES { + withName: 'PICARD_MARKDUPLICATES' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c0/c0d4bbb10417a70d137a28da09329d9f9fbdf964a1cfeda24b05b618cae6b16f/data' : 'community.wave.seqera.io/library/picard:3.1.1--c28da730a329ab3c' } } - withName: QUALIMAP_RNASEQ { + withName: 'QUALIMAP_RNASEQ' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7a/7aa0998788d327c6e7104c2c1e7bea2e8bb8fb7076ec5de3fdab4027e501b9a9/data' : 'community.wave.seqera.io/library/qualimap:2.3--8375b60bba97a2a6' } } - withName: SUBREAD_FEATURECOUNTS { + withName: 'SUBREAD_FEATURECOUNTS' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2a/2a81571bc8c4ac812adb76c51045a245041d7cc8923a2d7cc34a866588fead0c/data' : 'community.wave.seqera.io/library/subread:2.0.6--df9c6b502b57bb9c' } } - withName: MULTIQC { + withName: 'MULTIQC' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6e/6e97dcafc5915f90f863e70153f96bbe47963ebfd08383454d8bcd7263696e4e/data' : 'community.wave.seqera.io/library/multiqc:1.25.1--4062a515975cacba' } } - withName: STRINGTIE_STRINGTIE { + withName: 'STRINGTIE_STRINGTIE' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9ebc6b1a27262420a5739330d369086b0d8c941a43b81d3fd0f741045bb3d46f/data' : 'community.wave.seqera.io/library/stringtie:2.2.3--77d8df3265c94ba1' } } - withName: UNTAR { + withName: 'UNTAR' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } } - withName: FQ_SUBSAMPLE { + withName: 'FQ_SUBSAMPLE' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b0/b00189d4f7eed55199354a3dff8a9a535e1dfb3a2f4c97f5d0bf9e388105795e/data' : 'community.wave.seqera.io/library/fq:0.12.0--ad6857b304869ce9' } } - withName: DUPRADAR { + withName: 'DUPRADAR' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/10141f8fd43964316d04214a5f7d99a62e11cdbab5bd2fcd4f7c3c06eca9f2f6/data' : 'community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--f75495d6abf45328' } } - withName: SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT { + withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a7/a7d1ef576617b9790973bc9d178c4ef136a52b6337260c536cff6cd68f103b45/data' : 'community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--859858039875a2a5' } } - withName: STAR_GENOMEGENERATE { + withName: 'STAR_GENOMEGENERATE' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a2/a2d5226e4ce3dee8b29154c16a87d282d96c76e75b6678d032643902591586e2/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:1d1b7da208684cac' } } - withName: STAR_ALIGN { + withName: 'STAR_ALIGN' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a2/a2d5226e4ce3dee8b29154c16a87d282d96c76e75b6678d032643902591586e2/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:1d1b7da208684cac' } } - withName: TXIMETA_TXIMPORT { + withName: 'TXIMETA_TXIMPORT' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f8/f89ab1fef6e38e572ad1844d06f6d3d334d2b19a70c9e5d87bfc862b88728c23/data' : 'community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--3b0ca8a1710e2b2b' } } - withName: SORTMERNA { + withName: 'SORTMERNA' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f1/f161ea3d4083b7d8fcbf8524cb5ab69f386b4e36b771bb5abf9ccf8ab29e9775/data' : 'community.wave.seqera.io/library/sortmerna:4.3.7--4cc83a7bffbaaa61' } } - withName: PRESEQ_LCEXTRAP { + withName: 'PRESEQ_LCEXTRAP' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5ab535d5b4c88dc4837cab00919d4d5ea66dd4d6dc837d841886bef72145f435/data' : 'community.wave.seqera.io/library/preseq:3.2.0--80c9d2ffee38d3ac' } } - withName: BEDTOOLS_GENOMECOV { + withName: 'BEDTOOLS_GENOMECOV' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/519a920dacc643078823740486c40d30b9f555c493217d9f72db04901350e009/data' : 'community.wave.seqera.io/library/bedtools:2.31.1--efd79503b8c63422' } } - withName: BBMAP_BBSPLIT { + withName: 'BBMAP_BBSPLIT' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/63ca91c8bf7285296777de219e5d5a71d2a7de47599cbc94441aced7868a4f83/data' : 'community.wave.seqera.io/library/bbmap:39.10--908996c2fb304bec' } } - withName: FASTQC { + withName: 'FASTQC' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fd/fd39534bf298698cbe3ee4d4a6f1e73330ec4bca44c38dd9a4d06cb5ea838017/data' : 'community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a' } } - withName: KALLISTO_QUANT { + withName: 'KALLISTO_QUANT' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24655791b5db39ffdfffa8e5aeabfd11dda4553b5311ddb22e724c38b1591e8d/data' : 'community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } } - withName: KALLISTO_INDEX { + withName: 'KALLISTO_INDEX' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24655791b5db39ffdfffa8e5aeabfd11dda4553b5311ddb22e724c38b1591e8d/data' : 'community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } } - withName: SAMTOOLS_SORT { + withName: 'SAMTOOLS_SORT' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } - withName: SAMTOOLS_IDXSTATS { + withName: 'SAMTOOLS_IDXSTATS' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } - withName: SAMTOOLS_INDEX { + withName: 'SAMTOOLS_INDEX' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } - withName: SAMTOOLS_FLAGSTAT { + withName: 'SAMTOOLS_FLAGSTAT' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } - withName: SAMTOOLS_STATS { + withName: 'SAMTOOLS_STATS' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } - withName: CUSTOM_CATADDITIONALFASTA { + withName: 'CUSTOM_CATADDITIONALFASTA' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c1/c17acd739990ad12c06583f57b097014c2bde5a91d0977fd102864a82f95e136/data' : 'community.wave.seqera.io/library/python:3.12.2--0d47e6fe32e00784' } } - withName: CUSTOM_TX2GENE { + withName: 'CUSTOM_TX2GENE' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/60/6029f43341dc0bea31d14c2ce4c779d7a48dfed6ecb29ce1630b8378c560c490/data' : 'community.wave.seqera.io/library/python:3.10.4--d0dc5eb8ea72fa82' } } - withName: CUSTOM_GETCHROMSIZES { + withName: 'CUSTOM_GETCHROMSIZES' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } - withName: UMITOOLS_PREPAREFORRSEM { + withName: 'UMITOOLS_PREPAREFORRSEM' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } } - withName: UMITOOLS_EXTRACT { + withName: 'UMITOOLS_EXTRACT' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } } - withName: UMITOOLS_DEDUP { + withName: 'UMITOOLS_DEDUP' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } } - withName: GFFREAD { + withName: 'GFFREAD' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9e6db95013607b07689e38ee37a654d029236de77fdfde97fe1866f45d01e064/data' : 'community.wave.seqera.io/library/gffread:0.12.7--1577aa7c95340d9f' } } - withName: FASTP { + withName: 'FASTP' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7e/7ec6234f24305b9694b89de0352fff942ce1d68f840184020b0b9135bc54bda1/data' : 'community.wave.seqera.io/library/fastp:0.23.4--c1051f83dcae53f5' } } - withName: SALMON_QUANT { + withName: 'SALMON_QUANT' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b8/b8e3bcb1daa42497d0159cd5ae3b6d164b4470a972dd72d9d10b365fa166e5a4/data' : 'community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } } - withName: SALMON_INDEX { + withName: 'SALMON_INDEX' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b8/b8e3bcb1daa42497d0159cd5ae3b6d164b4470a972dd72d9d10b365fa166e5a4/data' : 'community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } } - withName: GUNZIP { + withName: 'GUNZIP' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } } - withName: TRIMGALORE { + withName: 'TRIMGALORE' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/10e7b91ef06bdf5790120809afc8cf36aac0261b618d810c952d5afd60dd5ed2/data' : 'community.wave.seqera.io/library/cutadapt_trim-galore:2aa2fc797328573b' } - } // - // Tools that do not have native Conda builds for AMD and ARM. Required custom builds in seqera Conda channel. + // Tools that do not have native Conda builds for AMD and ARM. Required custom builds in 'seqera' Conda channel. // - withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/18/18b787cb710e54b55e04d8df4f5d363b3581c0f6008a908d7ab7de03275dfedb/data' : 'community.wave.seqera.io/library/star_samtools_gawk:c0246261b9d809e1' } } withName: 'STAR_GENOMEGENERATE_IGENOMES' { - //conda = 'bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' - conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/18/18b787cb710e54b55e04d8df4f5d363b3581c0f6008a908d7ab7de03275dfedb/data' : 'community.wave.seqera.io/library/star_samtools_gawk:c0246261b9d809e1' } } withName: 'RSEM_PREPAREREFERENCE' { - //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' - conda = 'seqera::rsem=1.3.3 seqera::star=2.7.10a' container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3/data' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } } withName: 'RSEM_CALCULATEEXPRESSION' { - //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' - conda = 'seqera::rsem=1.3.3 seqera::star=2.7.10a' container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3/data' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } } @@ -253,13 +257,11 @@ process { // //withName: 'HISAT2_ALIGN' { - // conda = 'bioconda::hisat2 bioconda::samtools' - // //conda = 'bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1' + // conda = 'bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1' //} //withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { - // conda = 'bioconda::hisat2' - // //conda = 'bioconda::hisat2=2.2.1' + // conda = 'bioconda::hisat2=2.2.1' //} // withName: 'KRAKEN2_KRAKEN2' { From 251481f075e573ad2dba0e75366fd620999cf9c1 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 11:59:43 +0100 Subject: [PATCH 37/40] Fix syntax error --- conf/arm.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/arm.config b/conf/arm.config index c28d97099..8f84cdeb0 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -269,3 +269,4 @@ process { // withName: 'BRACKEN_BRACKEN' { // conda = 'bioconda::bracken=2.9' //} +} From f59132afa965188eed35d3504f6b6688b0d21599 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 12:28:10 +0000 Subject: [PATCH 38/40] revert trimgalore tweak to appease linter --- modules/nf-core/trimgalore/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 02f4b16ad..8a2fc54b3 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -4,7 +4,7 @@ process TRIMGALORE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.10--hdfd78af_1' : + 'https://depot.galaxyproject.org/singularity/trim-galore%3A0.6.10--hdfd78af_1' : 'biocontainers/trim-galore:0.6.10--hdfd78af_1' }" input: From 40f05c5dcaa50b911116e804d6510f8e34443635 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 12:28:23 +0000 Subject: [PATCH 39/40] Update pipeline-level tests --- tests/default.nf.test.snap | 18 +++++++++--------- tests/featurecounts_group_type.nf.test.snap | 18 +++++++++--------- tests/hisat2.nf.test.snap | 18 +++++++++--------- tests/kallisto.nf.test.snap | 18 +++++++++--------- tests/min_mapped_reads.nf.test.snap | 18 +++++++++--------- tests/remove_ribo_rna.nf.test.snap | 18 +++++++++--------- tests/salmon.nf.test.snap | 18 +++++++++--------- tests/skip_qc.nf.test.snap | 18 +++++++++--------- tests/star_rsem.nf.test.snap | 18 +++++++++--------- 9 files changed, 81 insertions(+), 81 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index d50bdafc0..b70ad3971 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -37,7 +37,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -90,7 +90,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T18:47:30.454374101" + "timestamp": "2024-10-23T10:43:40.33664602" }, "Params: default": { "content": [ @@ -212,7 +212,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -1300,18 +1300,18 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", - "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "multiqc_featurecounts_biotype_plot.txt:md5,5d83930a8c0aebf5fff0a5d12857b42d", "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1459,6 +1459,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T19:14:46.845308285" + "timestamp": "2024-10-23T10:42:45.202573855" } } \ No newline at end of file diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index d72672710..bbe39ddd6 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -37,7 +37,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -90,7 +90,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T18:52:01.516368536" + "timestamp": "2024-10-23T10:54:29.62339584" }, "Params: --featurecounts_group_type false": { "content": [ @@ -206,7 +206,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -1266,18 +1266,18 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", - "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1409,6 +1409,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T19:24:36.371474446" + "timestamp": "2024-10-23T10:53:28.969150716" } } \ No newline at end of file diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 62e0b952f..78d8c3ad4 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -35,7 +35,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "UNTAR_HISAT2_INDEX": { "untar": 1.34 @@ -91,7 +91,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T15:42:22.430556863" + "timestamp": "2024-10-23T11:01:31.33505759" }, "Params: --aligner hisat2": { "content": [ @@ -206,7 +206,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -1247,18 +1247,18 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,da5043f8ab9b5bd51d91ccf3111c655e", - "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "multiqc_featurecounts_biotype_plot.txt:md5,d784fc4b2dce860c8f88cc3e936e589e", "multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1309,6 +1309,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T15:41:24.698018172" + "timestamp": "2024-10-23T11:00:43.422573373" } } \ No newline at end of file diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index e48e6895f..8aea96806 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -47,7 +47,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -236,24 +236,24 @@ "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee", - "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233" + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T15:46:36.506804194" + "timestamp": "2024-10-23T11:04:57.579312846" }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ @@ -288,7 +288,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -329,6 +329,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T15:47:47.272256089" + "timestamp": "2024-10-23T11:05:54.052864085" } } \ No newline at end of file diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 2f4db1480..e11236066 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -119,7 +119,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -1041,19 +1041,19 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", - "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fail_mapped_samples_table.txt:md5,5dd9b06f326b1a55d78878343af89927", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "multiqc_featurecounts_biotype_plot.txt:md5,d0e3792631b78e393de8e6bbbb49d476", "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1175,7 +1175,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T19:45:32.241828903" + "timestamp": "2024-10-23T11:18:04.553985917" }, "Params: --min_mapped_reads 90 - stub": { "content": [ @@ -1215,7 +1215,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -1268,6 +1268,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T19:46:21.485818867" + "timestamp": "2024-10-23T11:19:22.443482528" } } \ No newline at end of file diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 789571cfb..79b4954b9 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -125,7 +125,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -1227,18 +1227,18 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,bfa9fd61367cd7265e324d009c974778", - "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "multiqc_featurecounts_biotype_plot.txt:md5,f4de303d3277d862031df94b509527ba", "multiqc_samtools_idxstats.txt:md5,58f19b28617037a2825f812d58d55e2e", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1386,7 +1386,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-22T12:24:58.795267716" + "timestamp": "2024-10-23T11:36:09.902195192" }, "Params: --remove_ribo_rna - stub": { "content": [ @@ -1429,7 +1429,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -1482,6 +1482,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-22T12:26:10.797017969" + "timestamp": "2024-10-23T11:37:11.90905171" } } \ No newline at end of file diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index a83151bbb..aa517a395 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -41,7 +41,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -281,17 +281,17 @@ "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,f789abe663d4b4214f0ddeb413a7f150", - "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -329,7 +329,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T16:22:14.604923669" + "timestamp": "2024-10-23T11:41:47.859384178" }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ @@ -361,7 +361,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -402,6 +402,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T16:23:12.380483903" + "timestamp": "2024-10-23T11:42:36.34114827" } } \ No newline at end of file diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index cb94364bb..0589bb509 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -34,7 +34,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -76,7 +76,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T20:14:28.433411196" + "timestamp": "2024-10-23T11:50:42.323505833" }, "Params: --skip_qc": { "content": [ @@ -154,7 +154,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -681,17 +681,17 @@ "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,ef51c78faebdd32bad296ba14406b41e", - "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -787,6 +787,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T20:13:44.078197492" + "timestamp": "2024-10-23T11:49:49.131172185" } } \ No newline at end of file diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index a68d337c2..c396c1a4a 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -116,7 +116,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -1138,18 +1138,18 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,5a68f7972ea275b21b12acdf43447dfb", - "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "multiqc_featurecounts_biotype_plot.txt:md5,aef45c9c7814f3127cd3e9b77a5ed676", "multiqc_samtools_idxstats.txt:md5,1cbc64fc9713831a6f45effc0cfe6a39", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1270,7 +1270,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T16:29:54.475156285" + "timestamp": "2024-10-23T12:16:02.205058346" }, "Params: --aligner star_rsem - stub": { "content": [ @@ -1305,7 +1305,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "UNTAR_RSEM_INDEX": { "untar": 1.34 @@ -1361,6 +1361,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T16:31:04.240180676" + "timestamp": "2024-10-23T12:17:33.292700445" } } \ No newline at end of file From 79370d35cac0f54f442e592ee52a36db61dfb96a Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 13:54:14 +0100 Subject: [PATCH 40/40] Update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5cde9cf6e..cacba7c82 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #1422](https://github.com/nf-core/rnaseq/pull/1422) - Bump lots of modules so that conda versions have ARM builds - [PR #1423](https://github.com/nf-core/rnaseq/pull/1423) - Bump STAR version for version with ARM Conda build - [PR #1424](https://github.com/nf-core/rnaseq/pull/1424) - Patch sortmerna to 4.3.7 for ARM compatibility +- [PR #1425](https://github.com/nf-core/rnaseq/pull/1425) - Add profile for ARM compatibility ## [[3.16.1](https://github.com/nf-core/rnaseq/releases/tag/3.16.1)] - 2024-10-16