From b3ded1fb16e47c41c38d949cca355ca1da70275b Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Fri, 3 Mar 2023 09:41:54 +0100
Subject: [PATCH] ARGS hicstuff bam2pairs
---
conf/hicstuff.config | 8 ++++++++
modules/local/hicstuff/bam2pairs.nf | 5 ++++-
2 files changed, 12 insertions(+), 1 deletion(-)
diff --git a/conf/hicstuff.config b/conf/hicstuff.config
index 578ded8..6f53691 100644
--- a/conf/hicstuff.config
+++ b/conf/hicstuff.config
@@ -126,6 +126,9 @@ params {
hicstuff_output_frags = 'fragments_list.txt'
hicstuff_frags_plot = 'False'
hicstuff_frags_plot_path = 'frags_hist.pdf'
+ hicstuff_valid_pairs = 'valid.pairs'
+ hicstuff_valid_idx = 'valid_idx.pairs'
+ hicstuff_min_qual = 30
}
process {
@@ -161,6 +164,11 @@ process {
}
withName: 'BAM2PAIRS' {
+ ext.args = { [
+ " -o ${params.hicstuff_valid_pairs}",
+ " -x ${params.hicstuff_valid_idx}",
+ " -q ${params.hicstuff_min_qual}"
+ ].join('').trim() }
publishDir = [
path: { "${params.outdir}/hicstuff/pairs" },
mode: 'copy'
diff --git a/modules/local/hicstuff/bam2pairs.nf b/modules/local/hicstuff/bam2pairs.nf
index 2e27360..68f7915 100644
--- a/modules/local/hicstuff/bam2pairs.nf
+++ b/modules/local/hicstuff/bam2pairs.nf
@@ -16,8 +16,11 @@ process BAM2PAIRS {
tuple val(meta1), path("valid_idx.pairs"), emit: idx_pairs
script:
+
+ def args = task.ext.args ?: ''
+
"""
- hicstuff_bam2pairs.py -b1 ${bam1} -b2 ${bam2} -o valid.pairs -x valid_idx.pairs -i ${info_contigs} -q 30 -e ${digestion} -f ${fasta}
+ hicstuff_bam2pairs.py -b1 ${bam1} -b2 ${bam2} -i ${info_contigs} -e ${digestion} -f ${fasta} ${args}
"""
}
--
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