From b1162124ca80ef5b6d2d8d9d495aa0d7b59b1c6f Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Fri, 6 May 2022 17:57:27 +0200
Subject: [PATCH] [MODIF] deal with technical replicates
---
subworkflows/local/hicpro.nf | 20 ++++++++++----------
subworkflows/local/input_check.nf | 15 +++++++++++++++
workflows/hic.nf | 27 +++------------------------
3 files changed, 28 insertions(+), 34 deletions(-)
diff --git a/subworkflows/local/hicpro.nf b/subworkflows/local/hicpro.nf
index f73fd95..cb6f33c 100644
--- a/subworkflows/local/hicpro.nf
+++ b/subworkflows/local/hicpro.nf
@@ -70,16 +70,16 @@ workflow HICPRO {
//**************************************
// MERGE AND REMOVE DUPLICATES
- if (params.split_fastq){
- ch_valid_pairs = ch_valid_pairs.map{ it -> removeChunks(it)}.groupTuple()
- ch_hicpro_stats = HICPRO_MAPPING.out.mapstats.map{it->removeChunks(it)}.groupTuple()
- .concat(HICPRO_MAPPING.out.pairstats.map{it->removeChunks(it)}.groupTuple(),
- ch_valid_stats.map{it->removeChunks(it)}.groupTuple())
- }else{
- ch_hicpro_stats = HICPRO_MAPPING.out.mapstats.groupTuple()
- .concat(HICPRO_MAPPING.out.pairstats.groupTuple(),
- ch_valid_stats.groupTuple())
- }
+ //if (params.split_fastq){
+ ch_valid_pairs = ch_valid_pairs.map{ it -> removeChunks(it)}.groupTuple()
+ ch_hicpro_stats = HICPRO_MAPPING.out.mapstats.map{it->removeChunks(it)}.groupTuple()
+ .concat(HICPRO_MAPPING.out.pairstats.map{it->removeChunks(it)}.groupTuple(),
+ ch_valid_stats.map{it->removeChunks(it)}.groupTuple())
+ //}else{
+ // ch_hicpro_stats = HICPRO_MAPPING.out.mapstats.groupTuple()
+ // .concat(HICPRO_MAPPING.out.pairstats.groupTuple(),
+ // ch_valid_stats.groupTuple())
+ //}
MERGE_VALID_INTERACTION (
ch_valid_pairs
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
index 999d1e3..d5cf6b2 100644
--- a/subworkflows/local/input_check.nf
+++ b/subworkflows/local/input_check.nf
@@ -30,6 +30,9 @@ workflow INPUT_CHECK {
.splitCsv ( header:true, sep:',' )
.map { create_fastq_channels(it) }
.map { it -> [it[0], [it[1], it[2]]]}
+ .groupTuple(by: [0])
+ .flatMap { it -> setMetaChunk(it) }
+ .collate(2)
.set { reads }
}
@@ -53,3 +56,15 @@ def create_fastq_channels(LinkedHashMap row) {
array = [ meta, file(row.fastq_1), file(row.fastq_2) ]
return array
}
+
+// Set the meta.chunk value in case of technical replicates
+def setMetaChunk(row){
+ def map = []
+ row[1].eachWithIndex() { file,i ->
+ meta = row[0].clone()
+ meta.chunks = i
+ map += [meta, file]
+ }
+ return map
+}
+
diff --git a/workflows/hic.nf b/workflows/hic.nf
index e71e3e9..4592e83 100644
--- a/workflows/hic.nf
+++ b/workflows/hic.nf
@@ -143,16 +143,6 @@ Channel.fromPath( params.fasta )
// Info required for completion email and summary
def multiqc_report = []
-def setMetaChunk(row){
- def map = []
- row[1].eachWithIndex() { file,i ->
- meta = row[0].clone()
- meta.chunks = i
- map += [meta, file]
- }
- return map
-}
-
workflow HIC {
ch_versions = Channel.empty()
@@ -163,19 +153,8 @@ workflow HIC {
INPUT_CHECK (
ch_input
)
- .reads
- //.map {
- // meta, fastq ->
- // meta.id = meta.id.split('_')[0..-2].join('_')
- // [ meta, fastq ] }
- .groupTuple(by: [0])
- .flatMap { it -> setMetaChunk(it) }
- .collate(2)
- .set { ch_fastq }
-
- ch_fastq.view()
- //INPUT_CHECK.out.reads.view()
+ INPUT_CHECK.out.reads.view()
//
// SUBWORKFLOW: Prepare genome annotation
@@ -190,7 +169,7 @@ workflow HIC {
// MODULE: Run FastQC
//
FASTQC (
- ch_fastq
+ INPUT_CHECK.out.reads
)
ch_versions = ch_versions.mix(FASTQC.out.versions)
@@ -198,7 +177,7 @@ workflow HIC {
// SUB-WORFLOW: HiC-Pro
//
HICPRO (
- ch_fastq,
+ INPUT_CHECK.out.reads,
PREPARE_GENOME.out.index,
PREPARE_GENOME.out.res_frag,
PREPARE_GENOME.out.chromosome_size,
--
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