From 4f3bd901f6f6ebc1488c0d3cd4dc7558800a0b14 Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Thu, 8 Jun 2023 09:31:42 +0200
Subject: [PATCH] correct path MarkDuplicates
---
modules/{nf-core/custom => local}/filterbam/main.nf | 0
modules/nf-core/custom/picard/markduplicates/main.nf | 4 +++-
subworkflows/local/hicstuff_sub.nf | 2 +-
3 files changed, 4 insertions(+), 2 deletions(-)
rename modules/{nf-core/custom => local}/filterbam/main.nf (100%)
diff --git a/modules/nf-core/custom/filterbam/main.nf b/modules/local/filterbam/main.nf
similarity index 100%
rename from modules/nf-core/custom/filterbam/main.nf
rename to modules/local/filterbam/main.nf
diff --git a/modules/nf-core/custom/picard/markduplicates/main.nf b/modules/nf-core/custom/picard/markduplicates/main.nf
index b89101b..eef8c81 100644
--- a/modules/nf-core/custom/picard/markduplicates/main.nf
+++ b/modules/nf-core/custom/picard/markduplicates/main.nf
@@ -31,13 +31,15 @@ process PICARD_MARKDUPLICATES {
avail_mem = (task.memory.mega*0.8).intValue()
}
"""
+ mv ${fasta} ${fasta.simpleName}.fasta
+
picard \\
-Xmx${avail_mem}M \\
MarkDuplicates \\
$args \\
--INPUT $bam \\
--OUTPUT ${prefix}.bam \\
- --REFERENCE_SEQUENCE $fasta \\
+ --REFERENCE_SEQUENCE ${fasta.simpleName}.fasta \\
--METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
diff --git a/subworkflows/local/hicstuff_sub.nf b/subworkflows/local/hicstuff_sub.nf
index f4ace14..9bb3406 100644
--- a/subworkflows/local/hicstuff_sub.nf
+++ b/subworkflows/local/hicstuff_sub.nf
@@ -11,7 +11,7 @@ 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_N } from '../../modules/nf-core/custom/samtools_n/sort/main'
-include { FILTER_PAIR } from '../../modules/nf-core/custom/filterbam/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'
--
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