From 5aaa26695842027ef53d871448b515659fac6e53 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 12 Apr 2019 16:15:39 +0200
Subject: [PATCH] kallisto: add verbose to indexing.nf
---
src/nf_modules/kallisto/indexing.nf | 2 ++
1 file changed, 2 insertions(+)
diff --git a/src/nf_modules/kallisto/indexing.nf b/src/nf_modules/kallisto/indexing.nf
index ea153569..76b168b2 100644
--- a/src/nf_modules/kallisto/indexing.nf
+++ b/src/nf_modules/kallisto/indexing.nf
@@ -10,6 +10,7 @@ Channel
process index_fasta {
tag "$fasta.baseName"
publishDir "results/mapping/index/", mode: 'copy'
+ echo true
input:
file fasta from fasta_file
@@ -20,6 +21,7 @@ process index_fasta {
script:
"""
+pwd
kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
2> ${fasta.baseName}_kallisto_report.txt
"""
--
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