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Merge pull request #486 from atrigila/csvtk_replace
Replace `CSVTK_JOIN` to improve processing in large amount of files
2 parents c06b188 + eab8687 commit 411a499

19 files changed

+187
-36
lines changed

‎CHANGELOG.md

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@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- [[#481]](https://github.com/nf-core/smrnaseq/pull/481) - Fix [MIRTOP_STATS IndexError](https://github.com/nf-core/smrnaseq/issues/477) - Fix mirtop process execution when mirgenedb is used.
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- [[#482]](https://github.com/nf-core/smrnaseq/pull/482) - Update documentation regarding MirgeneDB input files.
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- [[#486]](https://github.com/nf-core/smrnaseq/pull/486) - Replace `CSVTK_JOIN` to improve processing in large amount of files.
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## v2.4.0 - 2024-10-14 - Navy Iron Boxer
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‎bin/pivot_longer.R

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#!/usr/bin/env Rscript
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library(optparse)
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library(tidyr)
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library(vroom)
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option_list <- list(
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make_option(c("--input"), type = "character", help = "Input TSV file", metavar = "character"),
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make_option(c("--output"), type = "character", help = "Output CSV file", metavar = "character")
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)
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opt_parser <- OptionParser(option_list = option_list)
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opt <- parse_args(opt_parser)
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# Read CSV with vroom
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data <- vroom::vroom(opt$input, delim = "\t", col_types = c(.default = "c"))
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last_col <- names(data)[ncol(data)]
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# Convert from wide to long format
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long_data <- data %>%
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pivot_longer(
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cols = last_col,
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names_to = "Sample_ID",
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values_to = "Counts"
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)
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vroom_write(long_data, opt$output, delim = ",")
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‎bin/pivot_wider.R

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#!/usr/bin/env Rscript
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library(optparse)
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library(tidyr)
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library(vroom)
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library(dplyr)
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option_list <- list(
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make_option(c("--input"), type = "character", help = "Input CSV file in long format", metavar = "character"),
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make_option(c("--output"), type = "character", help = "Output CSV file in wide format", metavar = "character")
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)
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opt_parser <- OptionParser(option_list = option_list)
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opt <- parse_args(opt_parser)
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# Read CSV with vroom
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long_data <- vroom::vroom(opt$input, delim = ",",
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col_types = c(
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Counts = "d",
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.default = "c"
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))
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# Transform to wide format
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wide_data <- long_data %>%
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pivot_wider(
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names_from = Sample_ID,
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values_from = Counts,
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values_fill = 0
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)
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# Export wide format
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vroom_write(wide_data, opt$output, delim = "\t")

‎conf/modules.config

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]
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}
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withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:CSVTK_JOIN' {
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ext.args = "--fields 'UID,Read,miRNA,Variant,iso_5p,iso_3p,iso_add3p,iso_snp,iso_5p_nt,iso_3p_nt,iso_add3p_nt,iso_snp_nt' --tabs --outer-join --na \"0\" --out-delimiter \"\t\""
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ext.prefix = "joined_samples_mirtop"
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withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:PIVOT_LONGER' {
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publishDir = [ enabled: false ]
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}
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withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:PIVOT_WIDER' {
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publishDir = [
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path: { "${params.outdir}/mirna_quant/mirtop" },
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mode: params.publish_dir_mode,

‎modules/local/pivot/longer/environment.yml

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channels:
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- conda-forge
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dependencies:
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- conda-forge::r-optparse
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- conda-forge::r-tidyverse

‎modules/local/pivot/longer/main.nf

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process PIVOT_LONGER {
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tag"$meta.id"
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label 'process_single'
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conda "${moduleDir}/environment.yml"
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container "community.wave.seqera.io/library/r-optparse_r-tidyverse_r-vroom:3cbb224fea84a0e1"
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input:
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tuple val(meta), path(tsv)
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output:
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tuple val(meta), path("*_long.csv") , emit: csv
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path "versions.yml" , emit: versions
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script:
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"""
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pivot_longer.R \\
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--input ${tsv} \\
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--output ${meta.id}_long.csv
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
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tidyr: \$(Rscript -e "library(tidyr); cat(as.character(packageVersion('tidyr')))")
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optparse: \$(Rscript -e "library(optparse); cat(as.character(packageVersion('optparse')))")
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END_VERSIONS
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"""
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}

‎modules/local/pivot/wider/environment.yml

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channels:
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- conda-forge
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dependencies:
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- conda-forge::r-optparse
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- conda-forge::r-tidyverse

‎modules/local/pivot/wider/main.nf

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process PIVOT_WIDER {
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tag"$meta.id"
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label 'process_high'
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conda "${moduleDir}/environment.yml"
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container "community.wave.seqera.io/library/r-optparse_r-tidyverse_r-vroom:3cbb224fea84a0e1"
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input:
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tuple val(meta), path(csvs)
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output:
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tuple val(meta), path("*joined_samples_mirtop.tsv") , emit: csv
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path "versions.yml" , emit: versions
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script:
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"""
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awk 'NR == 1 || FNR > 1' ${csvs.join(' ')} > final_long_results_temp.csv
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pivot_wider.R \\
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--input final_long_results_temp.csv \\
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--output ${meta.id}_concatenated_temp.csv
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sort -t\$'\t' -k1,1 ${meta.id}_concatenated_temp.csv > joined_samples_mirtop.tsv
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
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tidyr: \$(Rscript -e "library(tidyr); cat(as.character(packageVersion('tidyr')))")
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dplyr: \$(Rscript -e "library(dplyr); cat(as.character(packageVersion('dplyr')))")
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optparse: \$(Rscript -e "library(optparse); cat(as.character(packageVersion('optparse')))")
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vroom: \$(Rscript -e "library(vroom); cat(as.character(packageVersion('vroom')))")
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END_VERSIONS
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"""
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}

‎subworkflows/local/mirna_quant.nf

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@@ -24,6 +24,9 @@ include { EDGER_QC } from '../../modules/local/edger_qc/main'
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include { BAM_STATS_MIRNA_MIRTOP } from '../../subworkflows/nf-core/bam_stats_mirna_mirtop/main'
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include { CSVTK_JOIN } from '../../modules/nf-core/csvtk/join/main'
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include { PIVOT_LONGER } from '../../modules/local/pivot/longer/main'
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include { PIVOT_WIDER } from '../../modules/local/pivot/wider/main'
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workflow MIRNA_QUANT {
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take:
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ch_reference_mature // channel: [ val(meta), fasta file]
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.collect{it[1]}
106109
.map{it -> return [[id:"TSVs"], it]}
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CSVTK_JOIN ( ch_tsvs )
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ch_versions = ch_versions.mix(CSVTK_JOIN.out.versions)
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PIVOT_LONGER( BAM_STATS_MIRNA_MIRTOP.out.counts )
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ch_versions = ch_versions.mix(PIVOT_LONGER.out.versions)
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ch_long_files = PIVOT_LONGER.out.csv
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.map { meta, file -> file }
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.collect()
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.map { files ->
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return [[id: "Long_Files"], files]
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}
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PIVOT_WIDER( ch_long_files )
122+
ch_versions = ch_versions.mix(PIVOT_WIDER.out.versions)
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DATATABLE_MERGE ( CSVTK_JOIN.out.csv )
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DATATABLE_MERGE ( PIVOT_WIDER.out.csv )
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ch_versions = ch_versions.mix(DATATABLE_MERGE.out.versions)
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ch_reads_genome = BOWTIE_MAP_HAIRPIN.out.fastq

‎tests/test_contamination_tech_reps.nf.test

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assertAll(
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{ assert workflow.success },
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{ assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
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{ assert workflow.trace.succeeded().size() == 100 },
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{ assert workflow.trace.succeeded().size() == 103 },
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{ assert snapshot(
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path("$outputDir/contaminant_filter/filter/Clone1_N1_trimmed.contamination_mqc.yaml").exists(), //TODO see if we can make these deterministic or why they are non-deterministic

‎tests/test_contamination_tech_reps.nf.test.snap

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},
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"software_versions": {
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"content": [
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"{BLAT_CDNA={blat=36}, BLAT_NCRNA={blat=36}, BOWTIE2_ALIGN_CDNA={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, BOWTIE2_ALIGN_NCRNA={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, BOWTIE2_ALIGN_TRNA={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, CAT_FASTQ={cat=8.3}, CSVTK_JOIN={csvtk=0.30.0}, DATATABLE_MERGE={r-base=3.6.2}, FASTP={fastp=0.23.4}, FILTER_STATS={BusyBox=1.32.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, GAWK_CDNA={gawk=5.3.0}, GAWK_NCRNA={gawk=5.3.0}, INDEX_CDNA={bowtie2=2.5.2}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, INDEX_NCRNA={bowtie2=2.5.2}, INDEX_TRNA={bowtie2=2.5.2}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, SEQKIT_GREP_CDNA={seqkit=2.8.0}, SEQKIT_GREP_NCRNA={seqkit=2.8.0}, STATS_GAWK_CDNA={gawk=5.3.0}, STATS_GAWK_NCRNA={gawk=5.3.0}, STATS_GAWK_TRNA={gawk=5.3.0}, Workflow={nf-core/smrnaseq=v2.4.0}}"
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"{BLAT_CDNA={blat=36}, BLAT_NCRNA={blat=36}, BOWTIE2_ALIGN_CDNA={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, BOWTIE2_ALIGN_NCRNA={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, BOWTIE2_ALIGN_TRNA={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, CAT_FASTQ={cat=8.3}, DATATABLE_MERGE={r-base=3.6.2}, FASTP={fastp=0.23.4}, FILTER_STATS={BusyBox=1.32.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, GAWK_CDNA={gawk=5.3.0}, GAWK_NCRNA={gawk=5.3.0}, INDEX_CDNA={bowtie2=2.5.2}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, INDEX_NCRNA={bowtie2=2.5.2}, INDEX_TRNA={bowtie2=2.5.2}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, PIVOT_LONGER={r-base=4.4.2, tidyr=1.3.1, optparse=1.7.5}, PIVOT_WIDER={r-base=4.4.2, tidyr=1.3.1, dplyr=1.1.4, optparse=1.7.5, vroom=1.6.5}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, SEQKIT_GREP_CDNA={seqkit=2.8.0}, SEQKIT_GREP_NCRNA={seqkit=2.8.0}, STATS_GAWK_CDNA={gawk=5.3.0}, STATS_GAWK_NCRNA={gawk=5.3.0}, STATS_GAWK_TRNA={gawk=5.3.0}, Workflow={nf-core/smrnaseq=v2.4.0}}"
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],
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"meta": {
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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"nextflow": "24.10.2"
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},
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"timestamp": "2024-10-08T23:16:26.853242481"
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"timestamp": "2024-12-10T00:29:32.052341"
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},
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"mirna_quant_bam": {
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"content": [
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6565
],
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"meta": {
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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"nextflow": "24.10.2"
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},
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"timestamp": "2024-10-01T20:06:04.974546479"
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"timestamp": "2024-12-10T00:29:32.116301175"
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},
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"mirna_quant_edger_qc": {
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"content": [
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],
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"meta": {
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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"nextflow": "24.10.2"
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},
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"timestamp": "2024-10-01T20:06:05.025175321"
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"timestamp": "2024-12-10T00:29:32.164075991"
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},
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"contaminant_filter_filter": {
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"content": [
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113113
],
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"meta": {
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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"nextflow": "24.10.2"
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},
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"timestamp": "2024-10-01T20:06:05.070939602"
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"timestamp": "2024-12-10T00:29:32.208602197"
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}
120-
}
120+
}

‎tests/test_mirgenedb.nf.test

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assertAll(
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{ assert workflow.success },
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{ assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
22-
{ assert workflow.trace.succeeded().size() == 104 },
22+
{ assert workflow.trace.succeeded().size() == 107 },
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{ assert workflow.trace.failed().size() == 1 },
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{ assert snapshot(

‎tests/test_mirgenedb.nf.test.snap

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},
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"software_versions": {
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"content": [
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"{BOWTIE_MAP_GENOME={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, CSVTK_JOIN={csvtk=0.30.0}, DATATABLE_MERGE={r-base=3.6.2}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRDEEP2_MAPPER={mirdeep2=2.0.1}, MIRDEEP2_MIRDEEP2={mirdeep2=2.0.1}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, SEQKIT_FQ2FA={seqkit=2.8.0}, SEQKIT_REPLACE={seqkit=2.8.0}, Workflow={nf-core/smrnaseq=v2.4.0}}"
22+
"{BOWTIE_MAP_GENOME={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, DATATABLE_MERGE={r-base=3.6.2}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRDEEP2_MAPPER={mirdeep2=2.0.1}, MIRDEEP2_MIRDEEP2={mirdeep2=2.0.1}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, PIVOT_LONGER={r-base=4.4.2, tidyr=1.3.1, optparse=1.7.5}, PIVOT_WIDER={r-base=4.4.2, tidyr=1.3.1, dplyr=1.1.4, optparse=1.7.5, vroom=1.6.5}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, SEQKIT_FQ2FA={seqkit=2.8.0}, SEQKIT_REPLACE={seqkit=2.8.0}, Workflow={nf-core/smrnaseq=v2.4.0}}"
2323
],
2424
"meta": {
2525
"nf-test": "0.9.0",
26-
"nextflow": "24.10.0"
26+
"nextflow": "24.10.2"
2727
},
28-
"timestamp": "2024-11-11T13:44:14.583324793"
28+
"timestamp": "2024-12-10T00:35:18.448206326"
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},
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"mirna_quant_bam": {
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"content": [

‎tests/test_nextflex.nf.test

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@@ -19,7 +19,7 @@ nextflow_pipeline {
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assertAll(
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{ assert workflow.success },
2121
{ assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
22-
{ assert workflow.trace.succeeded().size() == 79 },
22+
{ assert workflow.trace.succeeded().size() == 82 },
2323

2424
{ assert snapshot(
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path("$outputDir/mirna_quant/bam/mature/sample2_mature.sorted.idxstats"),

‎tests/test_nextflex.nf.test.snap

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},
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"software_versions": {
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"content": [
37-
"{BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, CSVTK_JOIN={csvtk=0.30.0}, DATATABLE_MERGE={r-base=3.6.2}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, Workflow={nf-core/smrnaseq=v2.4.0}}"
37+
"{BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, DATATABLE_MERGE={r-base=3.6.2}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, PIVOT_LONGER={r-base=4.4.2, tidyr=1.3.1, optparse=1.7.5}, PIVOT_WIDER={r-base=4.4.2, tidyr=1.3.1, dplyr=1.1.4, optparse=1.7.5, vroom=1.6.5}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, Workflow={nf-core/smrnaseq=v2.4.0}}"
3838
],
3939
"meta": {
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"nf-test": "0.9.0",
41-
"nextflow": "24.04.4"
41+
"nextflow": "24.10.2"
4242
},
43-
"timestamp": "2024-10-08T23:25:57.880948228"
43+
"timestamp": "2024-12-10T00:37:47.333537716"
4444
},
4545
"mirna_quant_bam": {
4646
"content": [
@@ -142,4 +142,4 @@
142142
},
143143
"timestamp": "2024-09-20T17:11:24.369706104"
144144
}
145-
}
145+
}

‎tests/test_skipfastp.nf.test

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -19,7 +19,7 @@ nextflow_pipeline {
1919
assertAll(
2020
{ assert workflow.success },
2121
{ assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
22-
{ assert workflow.trace.succeeded().size() == 64 },
22+
{ assert workflow.trace.succeeded().size() == 66 },
2323

2424
{ assert snapshot(
2525
path("$outputDir/mirna_quant/mirtop/joined_samples_mirtop.tsv").exists(),

‎tests/test_skipfastp.nf.test.snap

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -41,13 +41,13 @@
4141
},
4242
"software_versions": {
4343
"content": [
44-
"{BOWTIE_MAP_GENOME={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, CSVTK_JOIN={csvtk=0.30.0}, DATATABLE_MERGE={r-base=3.6.2}, FASTQC_RAW={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, Workflow={nf-core/smrnaseq=v2.4.0}}"
44+
"{BOWTIE_MAP_GENOME={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, DATATABLE_MERGE={r-base=3.6.2}, FASTQC_RAW={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, PIVOT_LONGER={r-base=4.4.2, tidyr=1.3.1, optparse=1.7.5}, PIVOT_WIDER={r-base=4.4.2, tidyr=1.3.1, dplyr=1.1.4, optparse=1.7.5, vroom=1.6.5}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, Workflow={nf-core/smrnaseq=v2.4.0}}"
4545
],
4646
"meta": {
4747
"nf-test": "0.9.0",
48-
"nextflow": "24.04.4"
48+
"nextflow": "24.10.2"
4949
},
50-
"timestamp": "2024-10-08T23:28:49.241105443"
50+
"timestamp": "2024-12-10T00:40:10.829696529"
5151
},
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"mirna_quant_bam": {
5353
"content": [
@@ -142,4 +142,4 @@
142142
},
143143
"timestamp": "2024-10-01T20:19:25.557700049"
144144
}
145-
}
145+
}

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