From 8be11d56d5de808a280e1a4af84aed80cead024f Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 23 Jul 2021 17:22:28 +0200
Subject: [PATCH] alntools: redirect stderr to report file
---
src/nf_modules/alntools/main.nf | 12 +++++++++---
1 file changed, 9 insertions(+), 3 deletions(-)
diff --git a/src/nf_modules/alntools/main.nf b/src/nf_modules/alntools/main.nf
index 26ba48f8..73a2278e 100644
--- a/src/nf_modules/alntools/main.nf
+++ b/src/nf_modules/alntools/main.nf
@@ -18,12 +18,18 @@ process bam2ec {
output:
tuple val(file_id), path("${bam.simpleName}.bin"), emit: bin
tuple val(gtf_id), path("${transcripts_lengths}"), emit: tsv
+ tuple val(file_id), path("${bam.simpleName}_bam2ec_report.txt"), emit: report
script:
"""
-cp ${bam} file_bam.bam
-cp ${bam_idx} file_bam.bam.bai
-alntools bam2ec ${params.bam2ec} -t ${transcripts_lengths} file_bam.bam ${bam.simpleName}.bin
+mkdir tmp
+alntools bam2ec \
+ -c 1 ${params.bam2ec} \
+ -d ./tmp \
+ -t ${transcripts_lengths} \
+ -v \
+ ${bam} ${bam.simpleName}.bin &> \
+ ${bam.simpleName}_bam2ec_report.txt
"""
}
--
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