From ada04928fc2e93fa7fa7676ef6191f79bc17ebb4 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Thu, 15 Apr 2021 16:29:41 +0200
Subject: [PATCH] [OUTPUT] change output organisation
---
main.nf | 58 +++++++++++++++++++++-----------------------
nextflow_schema.json | 4 +--
2 files changed, 29 insertions(+), 33 deletions(-)
diff --git a/main.nf b/main.nf
index 177050a..3ce53af 100644
--- a/main.nf
+++ b/main.nf
@@ -302,10 +302,7 @@ Channel.from(summary.collect{ [it.key, it.value] })
process get_software_versions {
publishDir "${params.outdir}/pipeline_info", mode: params.publish_dir_mode,
- saveAs: { filename ->
- if (filename.indexOf('.csv') > 0) filename
- else null
- }
+ saveAs: { filename -> if (filename.indexOf('.csv') > 0) filename else null }
output:
file 'software_versions_mqc.yaml' into ch_software_versions_yaml
@@ -331,7 +328,7 @@ if(!params.bwt2_index && params.fasta){
process makeBowtie2Index {
tag "$fasta_base"
label 'process_highmem'
- publishDir path: { params.save_reference ? "${params.outdir}/reference_genome" : params.outdir },
+ publishDir path: { params.save_reference ? "${params.outdir}/reference_genome" : params.outdir },
saveAs: { params.save_reference ? it : null }, mode: params.publish_dir_mode
input:
@@ -355,7 +352,7 @@ if(!params.chromosome_size && params.fasta){
process makeChromSize {
tag "$fasta"
label 'process_low'
- publishDir path: { params.save_reference ? "${params.outdir}/reference_genome" : params.outdir },
+ publishDir path: { params.save_reference ? "${params.outdir}/reference_genome" : params.outdir },
saveAs: { params.save_reference ? it : null }, mode: params.publish_dir_mode
input:
@@ -403,8 +400,8 @@ if(!params.restriction_fragments && params.fasta && !params.dnase){
process bowtie2_end_to_end {
tag "$sample"
label 'process_medium'
- publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/hicpro/mapping" : params.outdir },
- saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
+ publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping/bwt2_end2end" : params.outdir },
+ saveAs: { filename -> if (params.save_aligned_intermediates) filename }, mode: params.publish_dir_mode
input:
set val(sample), file(reads) from raw_reads
@@ -443,9 +440,9 @@ process bowtie2_end_to_end {
process trim_reads {
tag "$sample"
label 'process_low'
- publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/hicpro/mapping" : params.outdir },
- saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
-
+ publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping/bwt2_trimmed" : params.outdir },
+ saveAs: { filename -> if (params.save_aligned_intermediates) filename }, mode: params.publish_dir_mode
+
when:
!params.dnase
@@ -467,8 +464,8 @@ process trim_reads {
process bowtie2_on_trimmed_reads {
tag "$sample"
label 'process_medium'
- publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/hicpro/mapping" : params.outdir },
- saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
+ publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping/bwt2_trimmed" : params.outdir },
+ saveAs: { filename -> if (params.save_aligned_intermediates) filename }, mode: params.publish_dir_mode
when:
!params.dnase
@@ -496,8 +493,9 @@ if (!params.dnase){
process bowtie2_merge_mapping_steps{
tag "$prefix = $bam1 + $bam2"
label 'process_medium'
- publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/hicpro/mapping" : params.outdir },
- saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
+ publishDir "${params.outdir}/hicpro/mapping", mode: params.publish_dir_mode,
+ saveAs: { filename -> if (params.save_aligned_intermediates && filename.endsWith("stat")) "stats/$filename"
+ else if (params.save_aligned_intermediates) filename}
input:
set val(prefix), file(bam1), file(bam2) from end_to_end_bam.join( trimmed_bam ).dump(tag:'merge')
@@ -507,9 +505,7 @@ if (!params.dnase){
set val(oname), file("${prefix}.mapstat") into all_mapstat
script:
- //sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2|_1|_2)/
sample = prefix.toString() - ~/(_R1|_R2)/
- //tag = prefix.toString() =~/_R1|_val_1|_1/ ? "R1" : "R2"
tag = prefix.toString() =~/_R1/ ? "R1" : "R2"
oname = prefix.toString() - ~/(\.[0-9]+)$/
"""
@@ -539,8 +535,9 @@ if (!params.dnase){
process dnase_mapping_stats{
tag "$sample = $bam"
label 'process_medium'
- publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/hicpro/mapping" : params.outdir },
- saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
+ publishDir "${params.outdir}/hicpro/mapping", mode: params.publish_dir_mode,
+ saveAs: { filename -> if (params.save_aligned_intermediates && filename.endsWith("stat")) "stats/$filename"
+ else if (params.save_aligned_intermediates) filename}
input:
set val(prefix), file(bam) from end_to_end_bam
@@ -572,7 +569,7 @@ process combine_mates{
tag "$sample = $r1_prefix + $r2_prefix"
label 'process_low'
publishDir "${params.outdir}/hicpro/mapping", mode: params.publish_dir_mode,
- saveAs: {filename -> filename.indexOf(".pairstat") > 0 ? "stats/$filename" : "$filename"}
+ saveAs: {filename -> filename.endsWith(".pairstat") ? "stats/$filename" : "$filename"}
input:
set val(sample), file(aligned_bam) from bwt2_merged_bam.groupTuple().dump(tag:'mates')
@@ -608,7 +605,7 @@ if (!params.dnase){
tag "$sample"
label 'process_low'
publishDir "${params.outdir}/hicpro/valid_pairs", mode: params.publish_dir_mode,
- saveAs: {filename -> filename.indexOf(".stat") > 0 ? "stats/$filename" : "$filename"}
+ saveAs: {filename -> filename.endsWith("stat") ? "stats/$filename" : "$filename"}
input:
set val(sample), file(pe_bam) from paired_bam
@@ -647,7 +644,7 @@ else{
tag "$sample"
label 'process_low'
publishDir "${params.outdir}/hicpro/valid_pairs", mode: params.publish_dir_mode,
- saveAs: {filename -> filename.indexOf(".stat") > 0 ? "stats/$filename" : "$filename"}
+ saveAs: {filename -> filename.endsWith(".stat") ? "stats/$filename" : "$filename"}
input:
set val(sample), file(pe_bam) from paired_bam
@@ -678,11 +675,10 @@ else{
process remove_duplicates {
tag "$sample"
label 'process_highmem'
- publishDir "${params.outdir}/hicpro/valid_pairs", mode: params.publish_dir_mode,
- saveAs: {filename -> filename.indexOf(".stat") > 0 ? "stats/$sample/$filename" : "$filename"}
+ publishDir "${params.outdir}/hicpro/valid_pairs", mode: params.publish_dir_mode
input:
- set val(sample), file(vpairs) from valid_pairs.groupTuple().dump(tag:'final')
+ set val(sample), file(vpairs) from valid_pairs.groupTuple()
output:
set val(sample), file("*.allValidPairs") into ch_vpairs, ch_vpairs_cool
@@ -724,13 +720,13 @@ process remove_duplicates {
process merge_stats {
tag "$ext"
label 'process_low'
- publishDir "${params.outdir}/hicpro/stats/${sample}", mode: params.publish_dir_mode
+ publishDir "${params.outdir}/hicpro/", mode: params.publish_dir_mode
input:
set val(prefix), file(fstat) from all_mapstat.groupTuple().concat(all_pairstat.groupTuple(), all_rsstat.groupTuple())
output:
- file("mstats/${sample}/*") into all_mstats
+ file("stats/") into all_mstats
script:
sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2|_1|_2)/
@@ -738,8 +734,8 @@ process merge_stats {
if ( (fstat =~ /.pairstat/) ){ ext = "mpairstat" }
if ( (fstat =~ /.RSstat/) ){ ext = "mRSstat" }
"""
- mkdir -p mstats/${sample}
- merge_statfiles.py -f ${fstat} > mstats/${sample}/${prefix}.${ext}
+ mkdir -p stats/${sample}
+ merge_statfiles.py -f ${fstat} > stats/${sample}/${prefix}.${ext}
"""
}
@@ -828,7 +824,7 @@ process cooler_raw {
label 'process_medium'
publishDir "${params.outdir}/contact_maps/", mode: 'copy',
- saveAs: {filename -> filename.indexOf(".cool") > 0 ? "raw/cool/$filename" : "raw/txt/$filename"}
+ saveAs: {filename -> filename.endsWith(".cool") ? "raw/cool/$filename" : "raw/txt/$filename"}
input:
set val(sample), file(contacts), val(res) from cool_build.combine(map_res_cool)
@@ -851,7 +847,7 @@ process cooler_balance {
label 'process_medium'
publishDir "${params.outdir}/contact_maps/", mode: 'copy',
- saveAs: {filename -> filename.indexOf(".cool") > 0 ? "norm/cool/$filename" : "norm/txt/$filename"}
+ saveAs: {filename -> filename.endsWith(".cool") ? "norm/cool/$filename" : "norm/txt/$filename"}
when:
!params.skip_balancing
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 93591e7..849c92e 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -225,7 +225,7 @@
"description": "Resolution to build the maps (comma separated)"
},
"hicpro_maps": {
- "type": "string",
+ "type": "boolean",
"description": "Generate raw and normalized contact maps with HiC-Pro"
},
"ice_filter_low_count_perc": {
@@ -535,4 +535,4 @@
"$ref": "#/definitions/institutional_config_options"
}
]
-}
\ No newline at end of file
+}
--
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