From da24408fce8779a3fedfd3122fa2f012b65f532c Mon Sep 17 00:00:00 2001
From: vvanoost <vincent.vanoosthuyse@ens-lyon.fr>
Date: Tue, 24 Jul 2018 13:51:30 +0200
Subject: [PATCH] SAM tools
---
src/RNAseq_sen1D.nf | 10 ++--------
1 file changed, 2 insertions(+), 8 deletions(-)
diff --git a/src/RNAseq_sen1D.nf b/src/RNAseq_sen1D.nf
index 361028c..13269dd 100644
--- a/src/RNAseq_sen1D.nf
+++ b/src/RNAseq_sen1D.nf
@@ -157,17 +157,11 @@ fi
}
/* bams sorting */
+
process sort_bam {
- tag "${pair_id}.bam"
+ tag "$bam.baseName"
cpus 4
- input:
- file bam from bam_files
-
- output:
- file "*_sorted.bam" into sorted_bam_files
-
- script:
"""
samtools sort -@ ${task.cpus} -O BAM -o ${bam.baseName}_sorted.bam ${bam}
"""
--
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