From 70dc013fc2d94f3185a3b628f9479073e2b266bc Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 12 Apr 2019 16:47:13 +0200
Subject: [PATCH] kallisto: fix singularity tests
---
src/nf_modules/kallisto/tests.sh | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/nf_modules/kallisto/tests.sh b/src/nf_modules/kallisto/tests.sh
index f8816f0a..412a2975 100755
--- a/src/nf_modules/kallisto/tests.sh
+++ b/src/nf_modules/kallisto/tests.sh
@@ -21,20 +21,20 @@
if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/kallisto/indexing.nf \
-c src/nf_modules/kallisto/indexing.config \
- -profile docker \
+ -profile singularity \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-resume
./nextflow src/nf_modules/kallisto/mapping_single.nf \
-c src/nf_modules/kallisto/mapping_single.config \
- -profile docker \
+ -profile singularity \
--index "results/mapping/index/tiny_v2.index" \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
-resume
./nextflow src/nf_modules/kallisto/mapping_paired.nf \
-c src/nf_modules/kallisto/mapping_paired.config \
- -profile docker \
+ -profile singularity \
--index "results/mapping/index/tiny_v2.index" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-resume
--
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