From 81a9ff871896148174f05a8a53872767cc77f0df Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Tue, 5 Dec 2023 15:14:42 +0100
Subject: [PATCH] add hicstuff versions
---
modules/local/hicstuff/align_bowtie2.nf | 8 ++++++++
modules/local/hicstuff/fragment_enzyme.nf | 6 ++++++
subworkflows/local/hicstuff.nf | 5 +++++
workflows/hic.nf | 1 +
4 files changed, 20 insertions(+)
diff --git a/modules/local/hicstuff/align_bowtie2.nf b/modules/local/hicstuff/align_bowtie2.nf
index 188836d..210c0d4 100644
--- a/modules/local/hicstuff/align_bowtie2.nf
+++ b/modules/local/hicstuff/align_bowtie2.nf
@@ -13,6 +13,7 @@ process BOWTIE2_ALIGNMENT {
output:
tuple val(meta), path ("*.bam"), emit: bam
+ path "versions.yml", emit: versions
script:
def prefix = task.ext.prefix ?: "${meta.id}"
@@ -26,6 +27,13 @@ process BOWTIE2_ALIGNMENT {
bowtie2 $args -p $task.cpus -x \$INDEX -U $reads > ${prefix}.tmp
samtools view -F 2048 -h -@ $task.cpus ${prefix}.tmp | samtools sort -n -@ $task.cpus -o ${prefix}.bam -
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+ END_VERSIONS
"""
}
diff --git a/modules/local/hicstuff/fragment_enzyme.nf b/modules/local/hicstuff/fragment_enzyme.nf
index 855bf48..b6d044a 100644
--- a/modules/local/hicstuff/fragment_enzyme.nf
+++ b/modules/local/hicstuff/fragment_enzyme.nf
@@ -13,6 +13,7 @@ process FRAGMENT_ENZYME {
tuple val(meta), path(params.hicstuff_output_contigs) , emit: info_contigs
tuple val(meta), path(params.hicstuff_output_frags), emit: fragments_list
path("*.pdf"), optional: true
+ path "versions.yml", emit: versions
script:
@@ -20,6 +21,11 @@ process FRAGMENT_ENZYME {
"""
hicstuff_fragments.py -e ${digestion} -i ${fasta} ${args}
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ hicstuff: v3.1.3)
+ END_VERSIONS
"""
}
diff --git a/subworkflows/local/hicstuff.nf b/subworkflows/local/hicstuff.nf
index d9c60ab..0b3072e 100644
--- a/subworkflows/local/hicstuff.nf
+++ b/subworkflows/local/hicstuff.nf
@@ -42,6 +42,7 @@ workflow HICSTUFF {
chromosome_size
main:
+ ch_versions = Channel.empty()
// Align each mates separetly and add mates information in [meta]
ch_reads_r1 = reads.map{ it -> pairToSingle(it,"R1") }
@@ -52,11 +53,13 @@ workflow HICSTUFF {
ch_reads,
index.collect()
)
+ ch_versions = ch_versions.mix(BOWTIE2_ALIGNMENT.out.versions)
FRAGMENT_ENZYME(
digestion,
fasta
)
+ ch_versions = ch_versions.mix(FRAGMENT_ENZYME.out.versions)
if (params.filter_pcr && params.filter_pcr_picard ){
error "Error: filter_pcr and filter_pcr_picard can't both be true at the same time! Set one of them false in the config file"
@@ -68,6 +71,7 @@ workflow HICSTUFF {
index
)
FILTER_PCR_DUP.out.bam.set{ new_ch_bam }
+ ch_versions = ch_versions.mix(FILTER_PCR_DUP.out.versions)
}
else {
@@ -130,4 +134,5 @@ workflow HICSTUFF {
emit:
cool = BUILD_MATRIX_COOL_ALT.out.matrix
+ versions = ch_versions
}
diff --git a/workflows/hic.nf b/workflows/hic.nf
index 70c1f8d..6111170 100644
--- a/workflows/hic.nf
+++ b/workflows/hic.nf
@@ -230,6 +230,7 @@ workflow HIC {
)
ch_cool = HICSTUFF.out.cool
ch_mqc = Channel.empty()
+ ch_versions = ch_versions.mix(HICSTUFF.out.versions)
}
//
--
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