From b1dcaa1f21ef9ffd46288fdbdc6594a6287f6d58 Mon Sep 17 00:00:00 2001
From: vvanoost <vincent.vanoosthuyse@ens-lyon.fr>
Date: Wed, 1 Aug 2018 16:44:59 +0200
Subject: [PATCH] final corrections to SE pipeline
---
src/RNAseq_sen1D_bowtie2_SE.nf | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/src/RNAseq_sen1D_bowtie2_SE.nf b/src/RNAseq_sen1D_bowtie2_SE.nf
index 5ed1688..70accab 100644
--- a/src/RNAseq_sen1D_bowtie2_SE.nf
+++ b/src/RNAseq_sen1D_bowtie2_SE.nf
@@ -254,29 +254,29 @@ multiqc -f .
/* bams sorting */
process sort_bam {
- tag "$reads.baseName"
+ tag "$bam.baseName"
cpus 4
publishDir "results/mapping_SE/bams/", mode: 'copy'
input:
- set pair_id, file(bam) from bam_files
+ file bam from bam_files
output:
- set pair_id, "*_sorted.bam" into sorted_bam_files
+ file "*_sorted.bam" into sorted_bam_files
script:
"""
-samtools sort -@ ${task.cpus} -O BAM -o ${pair_id}_sorted.bam ${bam}
+samtools sort -@ ${task.cpus} -O BAM -o ${bam.baseName}_sorted.bam ${bam}
"""
}
/* bams indexing */
process index_bam {
- tag "$reads.baseName"
+ tag "$bam.baseName"
publishDir "results/mapping_SE/bams/", mode: 'copy'
input:
- set pair_id, file(bam) from sorted_bam_files
+ file bam from sorted_bam_files
output:
- set pair_id, "*bam*" into indexed_bam_file
+ file "*bam*" into indexed_bam_file
script:
"""
samtools index ${bam}
--
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