From cbf0b5449c8a99aef395fee7b42d2f29a16238da Mon Sep 17 00:00:00 2001
From: aliarifki <aliarifki@outlook.fr>
Date: Wed, 5 Jul 2023 15:12:03 +0200
Subject: [PATCH] Container pour start positoins count
---
src/nf_modules/samtools/main.nf | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index d44804b..854c4f1 100755
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -24,6 +24,7 @@ samtools sort -@ ${task.cpus} ${bam} -O BAM -o ${bam.simpleName}_sorted.bam
params.start_position_counts_out = ""
process start_position_counts {
+ container = "${container_url}"
tag "${barcode}"
label "big_mem_multi_cpus"
publishDir "results/${params.start_position_counts_out}", mode: 'copy'
@@ -37,10 +38,9 @@ process start_position_counts {
script:
"""
mkdir ${barcode}
-cd ${barcode}/
-samtools view -F 260 ../${bam} |
+samtools view -F 260 ${bam} |
cut -f 1,4 |
- sort > ${barcode}_start_positions_counts.txt
+ sort > ${barcode}/${barcode}_start_positions_counts.txt
"""
}
--
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