From b747108841d749f46385dc85a1b55fe1d0a282b4 Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Thu, 21 Sep 2023 09:28:24 +0200
Subject: [PATCH] add versions to filter pcr picard subworkflow
---
modules/local/filterbam/main.nf | 5 +++++
subworkflows/local/filter_pcr_dup.nf | 7 ++++++-
subworkflows/local/hicpro_mapping.nf | 7 ++-----
3 files changed, 13 insertions(+), 6 deletions(-)
diff --git a/modules/local/filterbam/main.nf b/modules/local/filterbam/main.nf
index 525c49a..22faaae 100644
--- a/modules/local/filterbam/main.nf
+++ b/modules/local/filterbam/main.nf
@@ -12,6 +12,7 @@ process FILTER_PAIR {
output:
tuple val(meta1), path("*_1paired.bam"), val(meta2), path("*_2paired.bam"), emit: bam
+ path "versions.yml" , emit: versions
script:
"""
@@ -21,5 +22,9 @@ process FILTER_PAIR {
samtools view -h -N common_reads.txt ${bam1} -O BAM > ${meta1.id}_1paired.bam
samtools view -h -N common_reads.txt ${bam2} -O BAM > ${meta2.id}_2paired.bam
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ END_VERSIONS
"""
}
diff --git a/subworkflows/local/filter_pcr_dup.nf b/subworkflows/local/filter_pcr_dup.nf
index cd5eece..740d11f 100644
--- a/subworkflows/local/filter_pcr_dup.nf
+++ b/subworkflows/local/filter_pcr_dup.nf
@@ -16,16 +16,19 @@ workflow FILTER_PCR_DUP {
index
main:
+ ch_versions = Channel.empty()
SAMTOOLS_SORT(
bam
)
+ ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions)
PICARD_MARKDUPLICATES(
SAMTOOLS_SORT.out.bam,
fasta.collect(),
index.collect()
)
+ ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions)
SAMTOOLS_SORT_N(
PICARD_MARKDUPLICATES.out.bam
@@ -40,9 +43,11 @@ workflow FILTER_PCR_DUP {
meta1.id == meta2.id && meta1.chunk == meta2.chunk && meta1.mates == "R1" && meta2.mates == "R2" ? [ meta1, bam1, meta2, bam2 ] : null
})
FILTER_PAIR.out.bam.set{ new_ch_bam }
-
+ ch_versions = ch_versions.mix(FILTER_PAIR.out.versions)
emit:
bam = new_ch_bam
+ versions = ch_versions
+
}
diff --git a/subworkflows/local/hicpro_mapping.nf b/subworkflows/local/hicpro_mapping.nf
index e544ebd..c219f5b 100644
--- a/subworkflows/local/hicpro_mapping.nf
+++ b/subworkflows/local/hicpro_mapping.nf
@@ -92,8 +92,6 @@ workflow HICPRO_MAPPING {
MERGE_BOWTIE2.out.bam
.set{ ch_bowtie2_merged }
- ch_bowtie2_merged.view()
-
ch_versions = ch_versions.mix(MERGE_BOWTIE2.out.versions)
ch_mapping_stats = MERGE_BOWTIE2.out.stats
@@ -113,9 +111,9 @@ workflow HICPRO_MAPPING {
.flatten()
.buffer( size: 2 )
.set {ch_bowtie2_merged}
+
+ ch_versions = ch_versions.mix(FILTER_PCR_DUP.out.versions)
}
- //TODO add versions
- ch_bowtie2_merged.view()
// Combine mates
ch_bowtie2_merged
@@ -123,7 +121,6 @@ workflow HICPRO_MAPPING {
.groupTuple()
.set {ch_bams}
- ch_bams.view()
}else{
--
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