From fa0b5e5eafd6cdb40d64437cc524325504fbda50 Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Tue, 13 Jun 2023 14:47:39 +0200
Subject: [PATCH] correct subworkflow filter pcr dup
---
conf/hicstuff.config | 1 +
subworkflows/local/hicstuff_sub.nf | 36 +++++-------------------------
2 files changed, 7 insertions(+), 30 deletions(-)
diff --git a/conf/hicstuff.config b/conf/hicstuff.config
index 3f5cdf6..f036e4c 100644
--- a/conf/hicstuff.config
+++ b/conf/hicstuff.config
@@ -350,6 +350,7 @@ profiles {
}
docker {
docker.enabled = true
+ docker.registry = 'quay.io'
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
diff --git a/subworkflows/local/hicstuff_sub.nf b/subworkflows/local/hicstuff_sub.nf
index 221d646..28d383e 100644
--- a/subworkflows/local/hicstuff_sub.nf
+++ b/subworkflows/local/hicstuff_sub.nf
@@ -8,11 +8,7 @@ include { BUILD_MATRIX_COOL_ALT } from '../../modules/local/hicstuff/build_matri
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 { SAMTOOLS_SORT } 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/local/filterbam/main'
-include { SAMTOOLS_INDEX } from '../../modules/nf-core/custom/samtools/index/main'
-include { PICARD_MARKDUPLICATES } from '../../modules/nf-core/custom/picard/markduplicates/main'
+include { FILTER_PCR_DUP } from './filter_pcr_dup'
// Paired-end to Single-end
def pairToSingle(row, mates) {
@@ -65,32 +61,12 @@ 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(
- BOWTIE2_ALIGNMENT.out.bam
+ FILTER_PCR_DUP(
+ BOWTIE2_ALIGNMENT.out.bam,
+ fasta,
+ index
)
-
-
- PICARD_MARKDUPLICATES(
- SAMTOOLS_SORT.out.bam,
- fasta.collect(),
- index.collect()
- )
-
- SAMTOOLS_SORT_N(
- PICARD_MARKDUPLICATES.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 }
-
+ FILTER_PCR_DUP.out.bam.set{ new_ch_bam }
}
else {
--
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