From 40694c85e85f493dd00fbba8f89ab9ac9025f148 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Mon, 5 Jun 2023 13:58:01 +0200
Subject: [PATCH] subworkflows/local/hicstuff_sub.nf: update
---
subworkflows/local/hicstuff_sub.nf | 49 +++++++++++++++---------------
1 file changed, 24 insertions(+), 25 deletions(-)
diff --git a/subworkflows/local/hicstuff_sub.nf b/subworkflows/local/hicstuff_sub.nf
index 69f04de..a27be24 100644
--- a/subworkflows/local/hicstuff_sub.nf
+++ b/subworkflows/local/hicstuff_sub.nf
@@ -9,8 +9,10 @@ include { FILTER_EVENT } from '../../modules/local/hicstuff/filter_event'
include { DISTANCE_LAW } from '../../modules/local/hicstuff/distance_law'
include { FILTER_PCR } from '../../modules/local/hicstuff/filter_pcr'
include { GATK4_MARKDUPLICATES } from '../../modules/nf-core/custom/gatk4/markduplicates/main'
-include { SAMTOOLS_SORT } from '../../modules/nf-core/custom/samtools/sort/main'
+include { SAMTOOLS_SORT as SAMTOOLS_SORT1} from '../../modules/nf-core/custom/samtools/sort/main'
+include { SAMTOOLS_SORT as SAMTOOLS_SORT2} from '../../modules/nf-core/custom/samtools/sort/main'
include { SAMTOOLS_SORT_N } from '../../modules/nf-core/custom/samtools_n/sort/main'
+include { FILTER_PAIR } from '../../modules/nf-core/custom/filterbam/main'
include { SAMTOOLS_INDEX } from '../../modules/nf-core/custom/samtools/index/main'
include { PICARD_MARKDUPLICATES } from '../../modules/nf-core/custom/picard/markduplicates/main'
@@ -65,27 +67,13 @@ workflow HICSTUFF_SUB {
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"
}
else if (params.filter_pcr_picard){
- SAMTOOLS_SORT(
+ SAMTOOLS_SORT1(
BOWTIE2_ALIGNMENT.out.bam
)
-/* GATK4_MARKDUPLICATES(
- SAMTOOLS_SORT.out.bam,
- fasta.map{ it[1] }.collect(),
- index.map{ it[1] }.collect()
- )
-
- SAMTOOLS_SORT_N(
- GATK4_MARKDUPLICATES.out.bam
- )
-
- SAMTOOLS_INDEX(
- SAMTOOLS_SORT_N.out.bam
- )
- */
PICARD_MARKDUPLICATES(
- SAMTOOLS_SORT.out.bam,
+ SAMTOOLS_SORT1.out.bam,
fasta.collect(),
index.collect()
)
@@ -94,24 +82,35 @@ workflow HICSTUFF_SUB {
PICARD_MARKDUPLICATES.out.bam
)
- SAMTOOLS_INDEX(
- SAMTOOLS_SORT_N.out.bam
- )
-
SAMTOOLS_SORT_N.out.bam.set{ ch_bam }
+ FILTER_PAIR(
+ ch_bam.combine(ch_bam)
+ .map {
+ meta1, bam1, meta2, bam2 ->
+ 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 }
+
}
else {
- BOWTIE2_ALIGNMENT.out.bam.set{ ch_bam }
+ // BOWTIE2_ALIGNMENT.out.bam.set{ ch_bam }
+ SAMTOOLS_SORT_N(BOWTIE2_ALIGNMENT.out.bam)
+ SAMTOOLS_SORT_N.out.bam.set{ ch_bam }
- }
- BAM2PAIRS(
ch_bam.combine(ch_bam)
.map {
meta1, bam1, meta2, bam2 ->
meta1.id == meta2.id && meta1.chunk == meta2.chunk && meta1.mates == "R1" && meta2.mates == "R2" ? [ meta1, bam1, meta2, bam2 ] : null
- },
+ }.set{ new_ch_bam }
+
+ }
+ new_ch_bam.view()
+
+ BAM2PAIRS(
+ new_ch_bam,
FRAGMENT_ENZYME.out.info_contigs.collect(),
digestion,
fasta.collect()
--
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