From 4142a52cfa192a544ed8212c46c1699e33aadc5c Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Fri, 20 Feb 2026 14:02:49 +0100 Subject: [PATCH 1/7] Remove unused modules + move PREPARE_GENOME to root main.nf --- main.nf | 107 +++++++++++------- modules.json | 10 -- modules/nf-core/bowtie2/build/environment.yml | 13 --- modules/nf-core/bowtie2/build/main.nf | 33 ------ modules/nf-core/bowtie2/build/meta.yml | 69 ----------- .../buildfromindex/environment.yml | 8 -- .../fastqscreen/buildfromindex/main.nf | 59 ---------- .../fastqscreen/buildfromindex/meta.yml | 57 ---------- nextflow.config | 9 +- nextflow_schema.json | 19 ++-- subworkflows/local/prepare_genome/main.nf | 6 +- .../local/prepare_genome/tests/main.nf.test | 6 +- workflows/seqinspector.nf | 57 ++++------ 13 files changed, 105 insertions(+), 348 deletions(-) delete mode 100644 modules/nf-core/bowtie2/build/environment.yml delete mode 100644 modules/nf-core/bowtie2/build/main.nf delete mode 100644 modules/nf-core/bowtie2/build/meta.yml delete mode 100644 modules/nf-core/fastqscreen/buildfromindex/environment.yml delete mode 100644 modules/nf-core/fastqscreen/buildfromindex/main.nf delete mode 100644 modules/nf-core/fastqscreen/buildfromindex/meta.yml diff --git a/main.nf b/main.nf index 47460d4d..10bb5d94 100644 --- a/main.nf +++ b/main.nf @@ -17,6 +17,7 @@ include { SEQINSPECTOR } from './workflows/seqinspector' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_seqinspector_pipeline' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_seqinspector_pipeline' +include { PREPARE_GENOME } from './subworkflows/local/prepare_genome' include { getGenomeAttribute } from 'plugin/nf-core-utils' /* @@ -25,47 +26,10 @@ include { getGenomeAttribute } from 'plugin/nf-core-utils' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -params.fasta = getGenomeAttribute('fasta') +params.fasta = getGenomeAttribute('fasta') +params.bwamem2 = getGenomeAttribute('bwamem2') +params.dict = getGenomeAttribute('dict') -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - NAMED WORKFLOWS FOR PIPELINE -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// -// WORKFLOW: Run main analysis pipeline depending on type of input -// -workflow NFCORE_SEQINSPECTOR { - take: - samplesheet // channel: samplesheet read in from --input - - main: - // - // WORKFLOW: Run pipeline - // - SEQINSPECTOR( - samplesheet, - params.bait_intervals, - params.bwamem2, - params.fasta ? channel.fromPath(params.fasta, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect() : channel.value([[:], []]), - params.fastq_screen_references, - params.multiqc_config, - params.multiqc_logo, - params.multiqc_methods_description, - params.outdir, - params.ref_dict, - params.run_picard_collecthsmetrics, - params.sample_size, - params.skip_tools ? params.skip_tools.split(',') : ['no_skip_tools'], - params.sort_bam, - params.target_intervals, - ) - - emit: - global_report = SEQINSPECTOR.out.global_report // channel: /path/to/multiqc_report.html - grouped_reports = SEQINSPECTOR.out.grouped_reports // channel: /path/to/multiqc_report.html -} /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RUN MAIN WORKFLOW @@ -74,6 +38,10 @@ workflow NFCORE_SEQINSPECTOR { workflow { + def fasta = params.fasta + ? channel.fromPath(params.fasta, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect() + : channel.value([[:], []]) + // // SUBWORKFLOW: Run initialisation tasks // @@ -90,11 +58,23 @@ workflow { params.show_hidden, ) + PREPARE_GENOME( + fasta, + params.bwamem2, + params.skip_tools ? params.skip_tools.split(',') : ['no_skip_tools'], + params.run_picard_collecthsmetrics, + params.dict, + ) + // // WORKFLOW: Run main workflow // NFCORE_SEQINSPECTOR( - PIPELINE_INITIALISATION.out.samplesheet + PIPELINE_INITIALISATION.out.samplesheet, + fasta, + PREPARE_GENOME.out.bwamem2_index, + PREPARE_GENOME.out.reference_dict, + PREPARE_GENOME.out.reference_fai, ) // // SUBWORKFLOW: Run completion tasks @@ -109,3 +89,48 @@ workflow { NFCORE_SEQINSPECTOR.out.global_report, ) } + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + NAMED WORKFLOWS FOR PIPELINE +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +// +// WORKFLOW: Run main analysis pipeline depending on type of input +// +workflow NFCORE_SEQINSPECTOR { + take: + samplesheet // channel: samplesheet read in from --input + fasta + bwamem2_index + dict + fasta_fai + + main: + // + // WORKFLOW: Run pipeline + // + SEQINSPECTOR( + samplesheet, + params.bait_intervals, + bwamem2_index, + fasta, + params.fastq_screen_references, + params.multiqc_config, + params.multiqc_logo, + params.multiqc_methods_description, + params.outdir, + dict, + fasta_fai, + params.run_picard_collecthsmetrics, + params.sample_size, + params.skip_tools ? params.skip_tools.split(',') : ['no_skip_tools'], + params.sort_bam, + params.target_intervals, + ) + + emit: + global_report = SEQINSPECTOR.out.global_report // channel: /path/to/multiqc_report.html + grouped_reports = SEQINSPECTOR.out.grouped_reports // channel: /path/to/multiqc_report.html +} diff --git a/modules.json b/modules.json index b18b2a73..e8f2421e 100644 --- a/modules.json +++ b/modules.json @@ -5,11 +5,6 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { - "bowtie2/build": { - "branch": "master", - "git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf", - "installed_by": ["modules"] - }, "bwamem2/index": { "branch": "master", "git_sha": "5dd46a36fca68d6ad1a6b22ec47adc8c6863717d", @@ -26,11 +21,6 @@ "git_sha": "3009f27c4e4b6e99da4eeebe82799e13924a4a1f", "installed_by": ["modules"] }, - "fastqscreen/buildfromindex": { - "branch": "master", - "git_sha": "ab2e7b785ee4fa6d108472862edbf983cea7db49", - "installed_by": ["modules"] - }, "fastqscreen/fastqscreen": { "branch": "master", "git_sha": "ab2e7b785ee4fa6d108472862edbf983cea7db49", diff --git a/modules/nf-core/bowtie2/build/environment.yml b/modules/nf-core/bowtie2/build/environment.yml deleted file mode 100644 index 066ff52e..00000000 --- a/modules/nf-core/bowtie2/build/environment.yml +++ /dev/null @@ -1,13 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -channels: - - conda-forge - - bioconda -dependencies: - # renovate: datasource=conda depName=bioconda/bowtie2 - - bioconda::bowtie2=2.5.4 - # renovate: datasource=conda depName=bioconda/htslib - - bioconda::htslib=1.21 - # renovate: datasource=conda depName=bioconda/samtools - - bioconda::samtools=1.21 - - conda-forge::pigz=2.8 diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf deleted file mode 100644 index 1be06ac8..00000000 --- a/modules/nf-core/bowtie2/build/main.nf +++ /dev/null @@ -1,33 +0,0 @@ -process BOWTIE2_BUILD { - tag "$fasta" - label 'process_high' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b41b403e81883126c3227fc45840015538e8e2212f13abc9ae84e4b98891d51c/data' : - 'community.wave.seqera.io/library/bowtie2_htslib_samtools_pigz:edeb13799090a2a6' }" - - input: - tuple val(meta), path(fasta) - - output: - tuple val(meta), path('bowtie2') , emit: index - tuple val("${task.process}"), val('bowtie2'), eval('bowtie2 --version 2>&1 | head -1 | sed "s/^.*bowtie2-align-s version //; s/ .*//"'), emit: versions_bowtie2, topic: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - """ - mkdir bowtie2 - bowtie2-build $args --threads $task.cpus $fasta bowtie2/${fasta.baseName} - """ - - stub: - """ - mkdir bowtie2 - touch bowtie2/${fasta.baseName}.{1..4}.bt2 - touch bowtie2/${fasta.baseName}.rev.{1,2}.bt2 - """ -} diff --git a/modules/nf-core/bowtie2/build/meta.yml b/modules/nf-core/bowtie2/build/meta.yml deleted file mode 100644 index 3a9d31cf..00000000 --- a/modules/nf-core/bowtie2/build/meta.yml +++ /dev/null @@ -1,69 +0,0 @@ -name: bowtie2_build -description: Builds bowtie index for reference genome -keywords: - - build - - index - - fasta - - genome - - reference -tools: - - bowtie2: - description: | - Bowtie 2 is an ultrafast and memory-efficient tool for aligning - sequencing reads to long reference sequences. - homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml - documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml - doi: 10.1038/nmeth.1923 - licence: ["GPL-3.0-or-later"] - identifier: "" -input: - - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file - ontologies: [] -output: - index: - - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - bowtie2: - type: directory - description: Bowtie2 genome index files - pattern: "*.bt2" - ontologies: [] - versions_bowtie2: - - - ${task.process}: - type: string - description: The name of the process - - bowtie2: - type: string - description: The name of the tool - - 'bowtie2 --version 2>&1 | head -1 | sed "s/^.*bowtie2-align-s version //; s/ .*//"': - type: eval - description: The expression to obtain the version of the tool - -topics: - versions: - - - ${task.process}: - type: string - description: The name of the process - - bowtie2: - type: string - description: The name of the tool - - 'bowtie2 --version 2>&1 | head -1 | sed "s/^.*bowtie2-align-s version //; s/ .*//"': - type: eval - description: The expression to obtain the version of the tool - -authors: - - "@joseespinosa" - - "@drpatelh" -maintainers: - - "@joseespinosa" - - "@drpatelh" diff --git a/modules/nf-core/fastqscreen/buildfromindex/environment.yml b/modules/nf-core/fastqscreen/buildfromindex/environment.yml deleted file mode 100644 index 9ff968c9..00000000 --- a/modules/nf-core/fastqscreen/buildfromindex/environment.yml +++ /dev/null @@ -1,8 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -channels: - - conda-forge - - bioconda -dependencies: - - bioconda::fastq-screen=0.16.0 - - bioconda::perl-gdgraph=1.54 diff --git a/modules/nf-core/fastqscreen/buildfromindex/main.nf b/modules/nf-core/fastqscreen/buildfromindex/main.nf deleted file mode 100644 index c543e61b..00000000 --- a/modules/nf-core/fastqscreen/buildfromindex/main.nf +++ /dev/null @@ -1,59 +0,0 @@ -process FASTQSCREEN_BUILDFROMINDEX { - label 'process_single' - - conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fc/fc53eee7ca23c32220a9662fbb63c67769756544b6d74a1ee85cf439ea79a7ee/data' - : 'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}" - - input: - val genome_names - path (indexes), stageAs: "dir*" - - output: - path ("FastQ_Screen_Genomes"), emit: database - tuple val("${task.process}"), val('fastqscreen'), eval('fastq_screen --version 2>&1 | sed "s/^.*FastQ Screen v//;"'), emit: versions_fastqscreen, topic: versions - - when: - task.ext.when == null || task.ext.when - - script: - dir = "FastQ_Screen_Genomes" - folder = indexes.collect { index -> index.toString() } - database = [genome_names, folder].transpose() - copy_indexes = folder.collect { index -> "cp -r ${index} ${dir}/${index}" }.join(" && ") - - // Folder name and index (within folder) name could be different - use bash to look for index name - config = database - .collect { index -> "########## ${index[0]} \nDATABASE ${index[0]} ${dir}/${index[1]}/${index[1] + '_to_be_replaced'}" } - .join("\n\n") - .replace("\n", "\\n") - - """ - mkdir ${dir} - ${copy_indexes} - - echo "${config}" > fastq_screen.conf - sed 's/\\\\n/\\n/g' fastq_screen.conf > ${dir}/fastq_screen.conf - echo "Replace folder name real index name" - - for f in ${folder.join(' ')} - do - TO_REPLACE=\${f}_to_be_replaced - - REPLACE_WITH=(\$f"/*.rev.1.bt2") - REPLACE_WITH=\$(basename \$REPLACE_WITH) - REPLACE_WITH=\${REPLACE_WITH%%.rev.1.bt2} - - sed "s/\$TO_REPLACE/\$REPLACE_WITH/g" ${dir}/fastq_screen.conf > new_conf.conf - mv new_conf.conf ${dir}/fastq_screen.conf - done - """ - - stub: - dir = "FastQ_Screen_Genomes" - """ - mkdir ${dir} - touch ${dir}/fastq_screen.conf - """ -} diff --git a/modules/nf-core/fastqscreen/buildfromindex/meta.yml b/modules/nf-core/fastqscreen/buildfromindex/meta.yml deleted file mode 100644 index 62561b2e..00000000 --- a/modules/nf-core/fastqscreen/buildfromindex/meta.yml +++ /dev/null @@ -1,57 +0,0 @@ -name: "fastqscreen_buildfromindex" -description: Build fastq screen config file from bowtie index files -keywords: - - build - - index - - genome - - reference -tools: - - "fastqscreen": - description: "FastQ Screen allows you to screen a library of sequences in FastQ - format against a set of sequence databases so you can see if the composition - of the library matches with what you expect." - homepage: "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/" - documentation: "https://stevenwingett.github.io/FastQ-Screen/" - tool_dev_url: "https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v0.15.3.zip" - doi: "10.5281/zenodo.5838377" - licence: - - "GPL-3.0-or-later" - identifier: "" -input: - - genome_names: - type: string - description: List of names for each index - - indexes: - type: directory - description: Bowtie2 genome directories containing index files -output: - database: - - FastQ_Screen_Genomes: - type: directory - description: fastq screen database folder containing config file and index - folders - pattern: "FastQ_Screen_Genomes" - versions_fastqscreen: - - - ${task.process}: - type: string - description: The name of the process - - fastqscreen: - type: string - description: The name of the tool - - fastq_screen --version 2>&1 | sed "s/^.*FastQ Screen v//;": - type: eval - description: The expression to obtain the version of the tool -topics: - versions: - - - ${task.process}: - type: string - description: The name of the process - - fastqscreen: - type: string - description: The name of the tool - - fastq_screen --version 2>&1 | sed "s/^.*FastQ Screen v//;": - type: eval - description: The expression to obtain the version of the tool -authors: - - "@snesic" - - "@JPejovicApis" diff --git a/nextflow.config b/nextflow.config index 40ca5ec9..341331ec 100644 --- a/nextflow.config +++ b/nextflow.config @@ -6,22 +6,19 @@ ---------------------------------------------------------------------------------------- */ -// Enable use of module binaries for e.g. module specific Python scripts -nextflow.enable.moduleBinaries = true - // Global default params, used in configs params { - // Input options input = null sample_size = 0 skip_tools = '' + // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false sort_bam = true - bwamem2 = null + // Fastqscreen options fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv" @@ -52,7 +49,6 @@ params { run_picard_collecthsmetrics = false bait_intervals = null target_intervals = null - ref_dict = null // Config options config_profile_name = null @@ -63,7 +59,6 @@ params { config_profile_contact = null config_profile_url = null - // Schema validation default options validate_params = true } diff --git a/nextflow_schema.json b/nextflow_schema.json index 404846c5..0332ca15 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -103,7 +103,16 @@ "exists": true, "fa_icon": "fas fa-copy", "description": "Path to BWA mem indices.", - "help_text": "If you wish to recompute indices available on igenomes, set `--bwa false`.\n\n> **NB** If none provided, will be generated automatically from the FASTA reference. Combine with `--save_reference` to save for future runs.\n\nIf you use AWS iGenomes, this has already been set for you appropriately." + "help_text": "If you wish to recompute indices available on igenomes, set `--bwamem2 false`.\n\n> **NB** If none provided, will be generated automatically from the FASTA reference.\n\nIf you use AWS iGenomes, this has already been set for you appropriately." + }, + "dict": { + "type": "string", + "hidden": true, + "description": "Sequence dictionary for the reference fasta file provided.", + "help_text": "If you wish to recompute indices available on igenomes, set `--ic false`.\n\n> **NB** If none provided, will be generated automatically from the FASTA reference.\n\nIf you use AWS iGenomes, this has already been set for you appropriately.", + "pattern": "^\\S+.dict$", + "format": "file-path", + "exists": true } } }, @@ -302,14 +311,6 @@ "pattern": "^\\S+.(bed|bed.gz|interval_list)$", "format": "file-path", "exists": true - }, - "ref_dict": { - "type": "string", - "hidden": true, - "description": "Sequence dictionary for the reference fasta file provided.", - "pattern": "^\\S+.dict$", - "format": "file-path", - "exists": true } } } diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index 3fe0bd39..176036b1 100644 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -52,7 +52,7 @@ workflow PREPARE_GENOME { } emit: - bwamem2_index = ch_bwamem2_index - reference_fai = ch_reference_fai - ref_dict = ch_ref_dict + bwamem2_index = ch_bwamem2_index + reference_fai = ch_reference_fai + reference_dict = ch_ref_dict } diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test index 3ba2985c..21fd5f50 100644 --- a/subworkflows/local/prepare_genome/tests/main.nf.test +++ b/subworkflows/local/prepare_genome/tests/main.nf.test @@ -32,7 +32,7 @@ nextflow_workflow { else if (key == "bwamem2_index") { return [key, val.collect { [path(it[1]).list().collect { it }] }] } - else if (key == "ref_dict") { + else if (key == "reference_dict") { return [key, val.collect { file(it[1]).name }] } return [key, val.collect { path(it[1]) }] @@ -66,7 +66,7 @@ nextflow_workflow { else if (key == "bwamem2_index") { return [key, val.collect { [path(it[1]).list().collect { it }] }] } - else if (key == "ref_dict") { + else if (key == "reference_dict") { return [key, val.collect { file(it[1]).name }] } return [key, val.collect { path(it[1]) }] @@ -100,7 +100,7 @@ nextflow_workflow { else if (key == "bwamem2_index") { return [key, val.collect { [path(it[1]).list().collect { it }] }] } - else if (key == "ref_dict") { + else if (key == "reference_dict") { return [key, val.collect { file(it[1]).name }] } return [key, val.collect { path(it[1]) }] diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf index 635e1a0b..79d7f536 100644 --- a/workflows/seqinspector.nf +++ b/workflows/seqinspector.nf @@ -5,29 +5,26 @@ */ // modules -include { BWAMEM2_MEM } from '../modules/nf-core/bwamem2/mem' -include { FASTQC } from '../modules/nf-core/fastqc' -include { FASTQSCREEN_FASTQSCREEN } from '../modules/nf-core/fastqscreen/fastqscreen' -include { MULTIQC as MULTIQC_GLOBAL } from '../modules/nf-core/multiqc' -include { MULTIQC as MULTIQC_PER_TAG } from '../modules/nf-core/multiqc' -include { PICARD_COLLECTMULTIPLEMETRICS } from '../modules/nf-core/picard/collectmultiplemetrics' -include { RUNDIRPARSER } from '../modules/local/rundirparser' -include { SAMTOOLS_FAIDX } from '../modules/nf-core/samtools/faidx' -include { SAMTOOLS_INDEX } from '../modules/nf-core/samtools/index' -include { SEQFU_STATS } from '../modules/nf-core/seqfu/stats' -include { SEQTK_SAMPLE } from '../modules/nf-core/seqtk/sample' +include { BWAMEM2_MEM } from '../modules/nf-core/bwamem2/mem' +include { FASTQC } from '../modules/nf-core/fastqc' +include { FASTQSCREEN_FASTQSCREEN } from '../modules/nf-core/fastqscreen/fastqscreen' +include { MULTIQC as MULTIQC_GLOBAL } from '../modules/nf-core/multiqc' +include { MULTIQC as MULTIQC_PER_TAG } from '../modules/nf-core/multiqc' +include { RUNDIRPARSER } from '../modules/local/rundirparser' +include { SAMTOOLS_INDEX } from '../modules/nf-core/samtools/index' +include { SEQFU_STATS } from '../modules/nf-core/seqfu/stats' +include { SEQTK_SAMPLE } from '../modules/nf-core/seqtk/sample' // subworkflow -include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome' -include { QC_BAM } from '../subworkflows/local/qc_bam' +include { QC_BAM } from '../subworkflows/local/qc_bam' // functions -include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline' -include { paramsSummaryMap } from 'plugin/nf-schema' -include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' -include { reportIndexMultiqc } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline' -include { samplesheetToList } from 'plugin/nf-schema' -include { softwareVersionsToYAML } from 'plugin/nf-core-utils' +include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { reportIndexMultiqc } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline' +include { samplesheetToList } from 'plugin/nf-schema' +include { softwareVersionsToYAML } from 'plugin/nf-core-utils' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -39,7 +36,7 @@ workflow SEQINSPECTOR { take: ch_samplesheet // channel: samplesheet read in from --input bait_intervals - bwamem2 + bwamem2_index fasta_reference fastq_screen_references multiqc_config @@ -47,6 +44,7 @@ workflow SEQINSPECTOR { multiqc_methods_description outdir ref_dict + ref_fai run_picard_collecthsmetrics sample_size skip_tools @@ -59,14 +57,6 @@ workflow SEQINSPECTOR { ch_bwamem2_mem = channel.empty() ch_samtools_index = channel.empty() - PREPARE_GENOME( - fasta_reference, - bwamem2, - skip_tools, - run_picard_collecthsmetrics, - ref_dict, - ) - // // MODULE: Parse rundir info // @@ -179,7 +169,7 @@ workflow SEQINSPECTOR { if (!("bwamem2_mem" in skip_tools)) { BWAMEM2_MEM( ch_sample, - PREPARE_GENOME.out.bwamem2_index, + bwamem2_index, fasta_reference, sort_bam ?: true, ) @@ -193,23 +183,18 @@ workflow SEQINSPECTOR { if (!("picard_collectmultiplemetrics" in skip_tools)) { - ch_reference_fai = PREPARE_GENOME.out.reference_fai - ch_bait_intervals = bait_intervals ? channel.fromPath(bait_intervals).collect() : channel.empty() ch_target_intervals = target_intervals ? channel.fromPath(target_intervals).collect() : channel.empty() - ch_ref_dict = PREPARE_GENOME.out.ref_dict - - QC_BAM( ch_bwamem2_mem, ch_samtools_index, fasta_reference, - ch_reference_fai, + ref_fai, run_picard_collecthsmetrics, ch_bait_intervals, ch_target_intervals, - ch_ref_dict, + ref_dict, ) ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics, QC_BAM.out.hs_metrics) From 9aec54d3bbffbce56048a0f3f295eae207e964fd Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Fri, 20 Feb 2026 14:03:52 +0100 Subject: [PATCH 2/7] Actually not using BOWTIE2 --- CITATIONS.md | 4 ---- README.md | 1 - subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf | 2 -- 3 files changed, 7 deletions(-) diff --git a/CITATIONS.md b/CITATIONS.md index 6d46e83b..6b025bee 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,10 +10,6 @@ ## Pipeline tools -- [Bowtie2](https://www.nature.com/articles/nmeth.1923) - - > Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012 Apr;9(4):357-9. doi: 10.1038/nmeth.1923. PubMed PMID: 22388286. - - [BWAMEM2](https://ieeexplore.ieee.org/abstract/document/8820962) > Vasimuddin Md, Misra S, Li H, Aluru S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. In: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS). IEEE; 2019:314-324. doi:10.1109/IPDPS.2019.00041 diff --git a/README.md b/README.md index 9c3da5b4..f48b9894 100644 --- a/README.md +++ b/README.md @@ -54,7 +54,6 @@ If provided, nf-core/seqinspector can also parse statistics from an Illumina run | Tool | Version | | ----------- | ------- | -| bowtie2 | 2.5.4 | | bwamem2 | 2.3 | | fastqc | 0.12.1 | | fastqscreen | 0.16.0 | diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf index 14748673..148a3959 100644 --- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf @@ -242,7 +242,6 @@ def genomeExistsError() { def toolCitationText() { def citation_text = [ "Tools used in the workflow included:", - "Bowtie2 (Langmead et al. 2012)", "BWAMEM2 (Vasimuddin et al. 2019)", "FastQC (Andrews 2010),", "FastQ Screen (Wingett & Andrews 2018)", @@ -259,7 +258,6 @@ def toolCitationText() { def toolBibliographyText() { def reference_text = [ - "
  • Langmead S., & Salzberg SL. (2012). Fast gapped-read alignment with Bowtie 2.
    • ", "
  • Vasimuddin Md., Misra S., Li H, & Aluru S. (2019). Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems.
    • ", "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
    • ", "
  • Wingett SW., & Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control. F1000Res. 2018 Aug 24 [revised 2018 Jan 1];7:1338. doi: 10.12688/f1000research.15931.2. eCollection
    • ", From ed8fa6618dc6b11ad9dbd5474ea0bba9de4a1947 Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Fri, 20 Feb 2026 14:04:53 +0100 Subject: [PATCH 3/7] CHANGELOG --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2ac691ec..ea501326 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -82,6 +82,8 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c - [#174](https://github.com/nf-core/seqinspector/pull/174) No params included in workflows - [#175](https://github.com/nf-core/seqinspector/pull/175) Update all modules and migrate the whole pipeline to using topic versions - [#176](https://github.com/nf-core/seqinspector/pull/176) No modules binaries +- [#177](https://github.com/nf-core/seqinspector/pull/177) Remove non used modules +- [#177](https://github.com/nf-core/seqinspector/pull/177) Move PREPARE_GENOME to the root main.nf script ### `Dependencies` From 6230afb4506d877e22c8a817f41303d02cb238de Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Fri, 20 Feb 2026 14:08:32 +0100 Subject: [PATCH 4/7] snapshot --- subworkflows/local/prepare_genome/tests/main.nf.test.snap | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap index 6b4bd3f0..4bb1683e 100644 --- a/subworkflows/local/prepare_genome/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_genome/tests/main.nf.test.snap @@ -13,7 +13,7 @@ ] ] ], - "ref_dict": [ + "reference_dict": [ "genome.dict" ], "reference_fai": [ @@ -21,7 +21,7 @@ ] } ], - "timestamp": "2026-02-20T11:14:59.592335797", + "timestamp": "2026-02-20T14:08:10.135732184", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -41,7 +41,7 @@ ] ] ], - "ref_dict": [ + "reference_dict": [ "reference.dict" ], "reference_fai": [ @@ -49,7 +49,7 @@ ] } ], - "timestamp": "2026-02-19T12:12:39.549105919", + "timestamp": "2026-02-20T14:07:30.247480534", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From e67261880f1dc425f1b272392733ce2ffe3e1926 Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Fri, 20 Feb 2026 14:24:52 +0100 Subject: [PATCH 5/7] regenerate snapshot --- tests/NovaSeq6000.nf.test.snap | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/NovaSeq6000.nf.test.snap b/tests/NovaSeq6000.nf.test.snap index 7d90acba..713edfa5 100644 --- a/tests/NovaSeq6000.nf.test.snap +++ b/tests/NovaSeq6000.nf.test.snap @@ -1032,8 +1032,6 @@ "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:MULTIQC_PER_TAG (2)", "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:MULTIQC_PER_TAG (3)", "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:MULTIQC_PER_TAG (4)", - "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:PREPARE_GENOME:BWAMEM2_INDEX (genome.fa)", - "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:PREPARE_GENOME:SAMTOOLS_FAIDX (genome.fa)", "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (Sample1_01)", "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (Sample23_03)", "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (SampleA_02)", @@ -1045,10 +1043,12 @@ "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:SAMTOOLS_INDEX (SampleA_02)", "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:SAMTOOLS_INDEX (Undetermined_05)", "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:SAMTOOLS_INDEX (sampletest_04)", - "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:SEQFU_STATS (seqfu)" + "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:SEQFU_STATS (seqfu)", + "[NXF_HASH] Submitted process > PREPARE_GENOME:BWAMEM2_INDEX (genome.fa)", + "[NXF_HASH] Submitted process > PREPARE_GENOME:SAMTOOLS_FAIDX (genome.fa)" ] ], - "timestamp": "2026-02-19T16:08:17.233872508", + "timestamp": "2026-02-20T14:19:24.909594023", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 94ea3cb2d2b9a785291ea8552c2e57ff52eef1b0 Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Fri, 20 Feb 2026 14:35:30 +0100 Subject: [PATCH 6/7] auto-format --- conf/base.config | 40 +-- conf/igenomes.config | 816 +++++++++++++++++++++--------------------- conf/modules.config | 65 ++-- conf/test.config | 7 +- conf/test_full.config | 4 +- nextflow.config | 206 +++++------ nf-test.config | 10 +- tests/nextflow.config | 3 +- 8 files changed, 576 insertions(+), 575 deletions(-) diff --git a/conf/base.config b/conf/base.config index 45099965..af915353 100644 --- a/conf/base.config +++ b/conf/base.config @@ -9,9 +9,9 @@ */ process { - cpus = { 1 * task.attempt } - memory = { 6.GB * task.attempt } - time = { 4.h * task.attempt } + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' } maxRetries = 1 @@ -23,36 +23,36 @@ process { // If possible, it would be nice to keep the same label naming convention when // adding in your local modules too. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors - withLabel:process_single { - cpus = { 1 } + withLabel: process_single { + cpus = { 1 } memory = { 6.GB * task.attempt } - time = { 4.h * task.attempt } + time = { 4.h * task.attempt } } - withLabel:process_low { - cpus = { 2 * task.attempt } + withLabel: process_low { + cpus = { 2 * task.attempt } memory = { 12.GB * task.attempt } - time = { 4.h * task.attempt } + time = { 4.h * task.attempt } } - withLabel:process_medium { - cpus = { 6 * task.attempt } + withLabel: process_medium { + cpus = { 6 * task.attempt } memory = { 36.GB * task.attempt } - time = { 8.h * task.attempt } + time = { 8.h * task.attempt } } - withLabel:process_high { - cpus = { 12 * task.attempt } + withLabel: process_high { + cpus = { 12 * task.attempt } memory = { 72.GB * task.attempt } - time = { 16.h * task.attempt } + time = { 16.h * task.attempt } } - withLabel:process_long { - time = { 20.h * task.attempt } + withLabel: process_long { + time = { 20.h * task.attempt } } - withLabel:process_high_memory { + withLabel: process_high_memory { memory = { 200.GB * task.attempt } } - withLabel:error_ignore { + withLabel: error_ignore { errorStrategy = 'ignore' } - withLabel:error_retry { + withLabel: error_retry { errorStrategy = 'retry' maxRetries = 2 } diff --git a/conf/igenomes.config b/conf/igenomes.config index 3f114377..9fb1acad 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -11,430 +11,430 @@ params { // illumina iGenomes reference file paths genomes { - 'GRCh37' { - fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed" - } - 'GRCh38' { - fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" - } - 'CHM13' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/" - bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf" - gff = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz" - mito_name = "chrM" - } - 'GRCm38' { - fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "1.87e9" - blacklist = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed" - } - 'TAIR10' { - fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt" - mito_name = "Mt" - } - 'EB2' { - fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt" + GRCh37 { + fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt" + mito_name = "MT" + macs_gsize = "2.7e9" + blacklist = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed" + } + GRCh38 { + fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed" + mito_name = "chrM" + macs_gsize = "2.7e9" + blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" + } + CHM13 { + fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/" + bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/" + gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf" + gff = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz" + mito_name = "chrM" + } + GRCm38 { + fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt" + mito_name = "MT" + macs_gsize = "1.87e9" + blacklist = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed" + } + TAIR10 { + fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt" + mito_name = "Mt" + } + EB2 { + fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt" } 'UMD3.1' { - fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt" - mito_name = "MT" - } - 'WBcel235' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed" - mito_name = "MtDNA" - macs_gsize = "9e7" + fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt" + mito_name = "MT" + } + WBcel235 { + fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed" + mito_name = "MtDNA" + macs_gsize = "9e7" } 'CanFam3.1' { - fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt" - mito_name = "MT" - } - 'GRCz10' { - fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'BDGP6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed" - mito_name = "M" - macs_gsize = "1.2e8" - } - 'EquCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt" - mito_name = "MT" - } - 'EB1' { - fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt" - } - 'Galgal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'Gm01' { - fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt" - } - 'Mmul_1' { - fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt" - mito_name = "MT" + fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt" + mito_name = "MT" + } + GRCz10 { + fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed" + mito_name = "MT" + } + BDGP6 { + fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed" + mito_name = "M" + macs_gsize = "1.2e8" + } + EquCab2 { + fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt" + mito_name = "MT" + } + EB1 { + fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt" + } + Galgal4 { + fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed" + mito_name = "MT" + } + Gm01 { + fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt" + } + Mmul_1 { + fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt" + mito_name = "MT" } 'IRGSP-1.0' { - fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed" - mito_name = "Mt" + fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed" + mito_name = "Mt" } 'CHIMP2.1.4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt" - mito_name = "MT" + fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt" + mito_name = "MT" } 'Rnor_5.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed" - mito_name = "MT" + fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed" + mito_name = "MT" } 'Rnor_6.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed" - mito_name = "MT" + fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed" + mito_name = "MT" } 'R64-1-1' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed" - mito_name = "MT" - macs_gsize = "1.2e7" - } - 'EF2' { - fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "1.21e7" - } - 'Sbi1' { - fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt" + fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed" + mito_name = "MT" + macs_gsize = "1.2e7" + } + EF2 { + fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt" + mito_name = "MT" + macs_gsize = "1.21e7" + } + Sbi1 { + fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt" } 'Sscrofa10.2' { - fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt" - mito_name = "MT" - } - 'AGPv3' { - fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed" - mito_name = "Mt" - } - 'hg38' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" - } - 'hg19' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg19-blacklist.bed" - } - 'mm10' { - fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "1.87e9" - blacklist = "${projectDir}/assets/blacklists/mm10-blacklist.bed" - } - 'bosTau8' { - fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed" - mito_name = "chrM" - } - 'ce10' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "9e7" - } - 'canFam3' { - fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt" - mito_name = "chrM" - } - 'danRer10' { - fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "1.37e9" - } - 'dm6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "1.2e8" - } - 'equCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt" - mito_name = "chrM" - } - 'galGal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt" - mito_name = "chrM" - } - 'panTro4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt" - mito_name = "chrM" - } - 'rn6' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed" - mito_name = "chrM" - } - 'sacCer3' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/" - readme = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "1.2e7" - } - 'susScr3' { - fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt" - mito_name = "chrM" + fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt" + mito_name = "MT" + } + AGPv3 { + fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed" + mito_name = "Mt" + } + hg38 { + fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed" + mito_name = "chrM" + macs_gsize = "2.7e9" + blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" + } + hg19 { + fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt" + mito_name = "chrM" + macs_gsize = "2.7e9" + blacklist = "${projectDir}/assets/blacklists/hg19-blacklist.bed" + } + mm10 { + fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt" + mito_name = "chrM" + macs_gsize = "1.87e9" + blacklist = "${projectDir}/assets/blacklists/mm10-blacklist.bed" + } + bosTau8 { + fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed" + mito_name = "chrM" + } + ce10 { + fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt" + mito_name = "chrM" + macs_gsize = "9e7" + } + canFam3 { + fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt" + mito_name = "chrM" + } + danRer10 { + fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed" + mito_name = "chrM" + macs_gsize = "1.37e9" + } + dm6 { + fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed" + mito_name = "chrM" + macs_gsize = "1.2e8" + } + equCab2 { + fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt" + mito_name = "chrM" + } + galGal4 { + fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt" + mito_name = "chrM" + } + panTro4 { + fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt" + mito_name = "chrM" + } + rn6 { + fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed" + mito_name = "chrM" + } + sacCer3 { + fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/" + readme = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt" + mito_name = "chrM" + macs_gsize = "1.2e7" + } + susScr3 { + fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/" + gtf = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed" + readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt" + mito_name = "chrM" } } } diff --git a/conf/modules.config b/conf/modules.config index 280b7b49..6b57399a 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -11,21 +11,20 @@ */ process { - publishDir = [ path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, mode: params.publish_dir_mode ] - withName: 'SEQTK_SAMPLE' { + withName: SEQTK_SAMPLE { ext.args = '-s100' } - withName: 'FASTQC' { + withName: FASTQC { ext.args = '--quiet' } - withName: 'SEQFU_STATS' { + withName: SEQFU_STATS { ext.args = '' publishDir = [ path: { "${params.outdir}/seqfu_stats" }, @@ -34,93 +33,91 @@ process { ] } - withName: 'BWAMEM2_INDEX' { + withName: BWAMEM2_INDEX { publishDir = [ path: { "${params.outdir}/bwamem2_index" }, mode: params.publish_dir_mode ] } - withName: 'PICARD_CREATESEQUENCEDICTIONARY' { + withName: PICARD_CREATESEQUENCEDICTIONARY { publishDir = [ path: { "${params.outdir}/picard_createsequencedictionary" }, mode: params.publish_dir_mode ] } - withName: 'BWAMEM2_MEM' { + withName: BWAMEM2_MEM { publishDir = [ path: { "${params.outdir}/bwamem2_mem" }, mode: params.publish_dir_mode ] } - withName: 'PICARD_COLLECTMULTIPLEMETRICS' { + withName: PICARD_COLLECTMULTIPLEMETRICS { publishDir = [ path: { "${params.outdir}/picard_collectmultiplemetrics" }, mode: params.publish_dir_mode ] } - withName: 'PICARD_COLLECTHSMETRICS' { + withName: PICARD_COLLECTHSMETRICS { + ext.args = { "--TMP_DIR ." } publishDir = [ path: { "${params.outdir}/picard_collecthsmetrics" }, mode: params.publish_dir_mode ] - ext.args = {"--TMP_DIR ."} } - withName: 'SAMTOOLS_FAIDX' { + withName: SAMTOOLS_FAIDX { publishDir = [ path: { "${params.outdir}/samtools_faidx" }, mode: params.publish_dir_mode ] } - withName: 'SAMTOOLS_INDEX' { + withName: SAMTOOLS_INDEX { publishDir = [ path: { "${params.outdir}/bwamem2_mem" }, mode: params.publish_dir_mode ] } - withName: 'RUNDIRPARSER' { + withName: RUNDIRPARSER { publishDir = [ path: { "${params.outdir}/rundirparser" }, mode: params.publish_dir_mode, - // The process _mqc.txt outputs should have identical names for the same sequencing platforms - // in order to be grouped together in the MultiQC report, but here we need to enforce uniqueness - // to avoid overwriting results in the publishDir. - saveAs: { filename -> "${meta.dirname}_${filename}" } - ] + saveAs: { filename -> "${meta.dirname}_${filename}" }] } - withName: 'MULTIQC_GLOBAL' { - ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } + withName: MULTIQC_GLOBAL { + ext.args = { params.multiqc_title ? "--title \"${params.multiqc_title}\"" : '' } publishDir = [ path: { "${params.outdir}/multiqc/global_report" }, mode: params.publish_dir_mode ] } - withName: 'MULTIQC_PER_TAG' { - ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } + withName: MULTIQC_PER_TAG { + ext.args = { params.multiqc_title ? "--title \"${params.multiqc_title}\"" : '' } publishDir = [ path: { "${params.outdir}/multiqc/group_reports" }, mode: params.publish_dir_mode, saveAs: { filename -> - if (filename == 'versions.yml') { - return null - } else if (filename =~/\[TAG:.+\]_multiqc_(report\.html|plots|data)/) { - def tag = (filename =~ /\[TAG:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1] - def new_filename = filename.replaceFirst( - "(?.*)\\[TAG:${tag}\\]_(?multiqc_(report\\.html|plots|data).*)", - '${prefix}${suffix}') - return "${tag}/${new_filename}" - } else { - return filename - } + if (filename == 'versions.yml') { + return null } - ] + else if (filename =~ /\[TAG:.+\]_multiqc_(report\.html|plots|data)/) { + def tag = (filename =~ /\[TAG:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1] + def new_filename = filename.replaceFirst( + "(?.*)\\[TAG:${tag}\\]_(?multiqc_(report\\.html|plots|data).*)", + '${prefix}${suffix}', + ) + return "${tag}/${new_filename}" + } + else { + return filename + } + }] } } diff --git a/conf/test.config b/conf/test.config index cb8f1ada..4ab15ba5 100644 --- a/conf/test.config +++ b/conf/test.config @@ -15,11 +15,11 @@ params { config_profile_description = 'Minimal test dataset to check pipeline function' // Input data - input = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv' - fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv" + input = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv' + fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv" // Genome references - genome = 'R64-1-1' + genome = 'R64-1-1' } process { @@ -28,5 +28,4 @@ process { memory: '8.GB', time: '1.h' ] - } diff --git a/conf/test_full.config b/conf/test_full.config index 65f0a532..d9ea691c 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -16,8 +16,8 @@ params { config_profile_description = 'Full test dataset to check pipeline function' // Input data for full size test - input = params.pipelines_testdata_base_path + 'seqinspector/full_tests/SampleSheet.csv' + input = params.pipelines_testdata_base_path + 'seqinspector/full_tests/SampleSheet.csv' // Genome references - genome = 'R64-1-1' + genome = 'R64-1-1' } diff --git a/nextflow.config b/nextflow.config index 341331ec..6f51793f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -9,25 +9,25 @@ // Global default params, used in configs params { // Input options - input = null - sample_size = 0 - skip_tools = '' + input = null + sample_size = 0 + skip_tools = '' // References - genome = null - igenomes_base = 's3://ngi-igenomes/igenomes/' - igenomes_ignore = false - sort_bam = true + genome = null + igenomes_base = 's3://ngi-igenomes/igenomes/' + igenomes_ignore = false + sort_bam = true // Fastqscreen options - fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv" + fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv" // MultiQC options - multiqc_config = null - multiqc_title = null - multiqc_logo = null - max_multiqc_email_size = '25.MB' - multiqc_methods_description = null + multiqc_config = null + multiqc_title = null + multiqc_logo = null + max_multiqc_email_size = '25.MB' + multiqc_methods_description = null // Boilerplate options outdir = null @@ -43,24 +43,24 @@ params { version = false modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' - trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') + trace_report_suffix = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') // picard_collecthsmetrics options - run_picard_collecthsmetrics = false - bait_intervals = null - target_intervals = null + run_picard_collecthsmetrics = false + bait_intervals = null + target_intervals = null // Config options - config_profile_name = null - config_profile_description = null + config_profile_name = null + config_profile_description = null - custom_config_version = 'master' - custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" - config_profile_contact = null - config_profile_url = null + custom_config_version = 'master' + custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" + config_profile_contact = null + config_profile_url = null // Schema validation default options - validate_params = true + validate_params = true } // Load base.config by default for all pipelines @@ -68,40 +68,40 @@ includeConfig 'conf/base.config' profiles { debug { - dumpHashes = true - process.beforeScript = 'echo $HOSTNAME' - cleanup = false + dumpHashes = true + process.beforeScript = 'echo $HOSTNAME' + cleanup = false nextflow.enable.configProcessNamesValidation = true } conda { - conda.enabled = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - conda.channels = ['conda-forge', 'bioconda'] - apptainer.enabled = false + conda.enabled = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + conda.channels = ['conda-forge', 'bioconda'] + apptainer.enabled = false } mamba { - conda.enabled = true - conda.useMamba = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + conda.enabled = true + conda.useMamba = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } docker { - docker.enabled = true - conda.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false - docker.runOptions = '-u $(id -u):$(id -g)' + docker.enabled = true + conda.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false + docker.runOptions = '-u $(id -u):$(id -g)' } arm64 { process.arch = 'arm64' @@ -115,54 +115,54 @@ profiles { wave.strategy = 'conda,container' } emulate_amd64 { - docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { - singularity.enabled = true - singularity.autoMounts = true - conda.enabled = false - docker.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + singularity.enabled = true + singularity.autoMounts = true + conda.enabled = false + docker.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } podman { - podman.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + podman.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } shifter { - shifter.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + shifter.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } charliecloud { - charliecloud.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - apptainer.enabled = false + charliecloud.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + apptainer.enabled = false } apptainer { - apptainer.enabled = true - apptainer.autoMounts = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false + apptainer.enabled = true + apptainer.autoMounts = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false } wave { apptainer.ociAutoPull = true @@ -172,12 +172,16 @@ profiles { wave.strategy = 'conda,container' } gpu { - docker.runOptions = '-u $(id -u):$(id -g) --gpus all' - apptainer.runOptions = '--nv' - singularity.runOptions = '--nv' + docker.runOptions = '-u $(id -u):$(id -g) --gpus all' + apptainer.runOptions = '--nv' + singularity.runOptions = '--nv' + } + test { + includeConfig 'conf/test.config' + } + test_full { + includeConfig 'conf/test_full.config' } - test { includeConfig 'conf/test.config' } - test_full { includeConfig 'conf/test_full.config' } } // Load nf-core custom profiles from different institutions @@ -193,10 +197,10 @@ includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !pa // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled // Set to your registry if you have a mirror of containers -apptainer.registry = 'quay.io' -docker.registry = 'quay.io' -podman.registry = 'quay.io' -singularity.registry = 'quay.io' +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' charliecloud.registry = 'quay.io' // Load igenomes.config if required @@ -251,7 +255,7 @@ manifest { affiliation: 'Pixelgen Technologies', github: 'Aratz', contribution: ['author'], - orcid: '0000-0003-2702-1103' + orcid: '0000-0003-2702-1103', ], [ name: 'Alfred Kedhammar', @@ -303,7 +307,7 @@ manifest { affiliation: 'National Bioinformatics Infrastructure Sweden', github: 'mahesh-panchal', contribution: ['contributor'], - orcid: '0000-0003-1675-0677' + orcid: '0000-0003-1675-0677', ], [ name: 'Ramprasad Neethiraj', @@ -413,7 +417,7 @@ plugins { validation { defaultIgnoreParams = ["genomes"] - monochromeLogs = params.monochrome_logs + monochromeLogs = params.monochrome_logs } // Load modules.config for DSL2 module specific options diff --git a/nf-test.config b/nf-test.config index 6a25cc8c..3b7f95dc 100644 --- a/nf-test.config +++ b/nf-test.config @@ -1,21 +1,21 @@ config { // location for all nf-test tests - testsDir = "." + testsDir = "." // nf-test directory including temporary files for each test - workDir = System.getenv("NFT_WORKDIR") ?: ".nf-test" + workDir = System.getenv("NFT_WORKDIR") ?: ".nf-test" // location of an optional nextflow.config file specific for executing tests configFile = "tests/nextflow.config" // ignore tests coming from the nf-core/modules repo - ignore = ['modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*'] + ignore = ['modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*'] // run all test with defined profile(s) from the main nextflow.config - profile ="test" + profile = "test" // list of filenames or patterns that should be trigger a full test run - triggers = ['nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore'] + triggers = ['nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore'] // load the necessary plugins plugins { diff --git a/tests/nextflow.config b/tests/nextflow.config index 5d979d45..8d6d7704 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -4,4 +4,5 @@ ======================================================================================== */ -aws.client.anonymous = true // fixes S3 access issues on self-hosted runners +// fixes S3 access issues on self-hosted runners +aws.client.anonymous = true From af5b83297739be39f09e33a594848a24af6d24c8 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Fri, 20 Feb 2026 14:44:00 +0100 Subject: [PATCH 7/7] Apply suggestion from @maxulysse --- conf/modules.config | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 6b57399a..f84f48ff 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -84,7 +84,10 @@ process { } withName: RUNDIRPARSER { - publishDir = [ + // The process _mqc.txt outputs should have identical names for the same sequencing platforms + // in order to be grouped together in the MultiQC report, but here we need to enforce uniqueness + // to avoid overwriting results in the publishDir. + publishDir = [ path: { "${params.outdir}/rundirparser" }, mode: params.publish_dir_mode, saveAs: { filename -> "${meta.dirname}_${filename}" }]