From 76661338cf8257793c6b87e638ca8107cf0de3b7 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 20 Aug 2021 15:36:56 +0200
Subject: [PATCH] emase-zero: redirect stdrr to report file
---
src/nf_modules/emase-zero/main.nf | 12 +++++++++---
1 file changed, 9 insertions(+), 3 deletions(-)
diff --git a/src/nf_modules/emase-zero/main.nf b/src/nf_modules/emase-zero/main.nf
index 6c8282ab..58cb0788 100644
--- a/src/nf_modules/emase-zero/main.nf
+++ b/src/nf_modules/emase-zero/main.nf
@@ -29,7 +29,7 @@ process emase {
label "big_mem_mono_cpus"
tag "$file_id"
if (params.count_out != "") {
- publishDir "results/${params.count_out}", mode: 'copy'
+ publishDir "results/counts/${params.count_out}", mode: 'copy'
}
input:
@@ -39,7 +39,8 @@ process emase {
tuple val(gene_to_transcript_id), path(gene_to_transcript)
output:
- tuple val(file_id), path("${bin.simpleName}.quantified"), emit: count
+ tuple val(file_id), path("${bin.simpleName}.quantified*"), emit: count
+ path "*_report.txt", emit: report
script:
"""
@@ -49,6 +50,11 @@ emase-zero ${params.count} \
-o ${bin.simpleName}.quantified \
-l ${transcript_length} \
-g gene_to_transcript.txt \
- ${bin}
+ ${bin} 2> ${file_prefix}_emase-zero_repport.txt
+
+if grep -q "ERROR" ${file_prefix}_emase-zero_repport.txt; then
+ exit 1
+fi
+
"""
}
\ No newline at end of file
--
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