From 099b8b5eab44f4701ddc7bb1347e931f7105bd45 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Thu, 7 Mar 2019 10:02:56 +0100
Subject: [PATCH] rsem: fix tests
---
src/nf_modules/rsem/quantification_single.nf | 3 +--
src/nf_modules/rsem/tests.sh | 4 ++--
2 files changed, 3 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/rsem/quantification_single.nf b/src/nf_modules/rsem/quantification_single.nf
index fe635ca8..bacba6b3 100644
--- a/src/nf_modules/rsem/quantification_single.nf
+++ b/src/nf_modules/rsem/quantification_single.nf
@@ -24,7 +24,7 @@ process mapping_fastq {
input:
set file_id, file(reads) from fastq_files
- file index from index_files.toList()
+ file index from index_files.collect()
output:
file "*" into count_files
@@ -37,7 +37,6 @@ process mapping_fastq {
}
}
"""
-ls -l
rsem-calculate-expression --bowtie2 \
--bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
--bowtie2-sensitivity-level "very_sensitive" \
diff --git a/src/nf_modules/rsem/tests.sh b/src/nf_modules/rsem/tests.sh
index 13256a52..e4cd2726 100755
--- a/src/nf_modules/rsem/tests.sh
+++ b/src/nf_modules/rsem/tests.sh
@@ -9,7 +9,7 @@
-c src/nf_modules/rsem/quantification_single.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index*" \
- --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+ --fastq "data/tiny_dataset/fastq/tiny*_R1.fastq" \
-resume
./nextflow src/nf_modules/rsem/quantification_paired.nf \
@@ -32,7 +32,7 @@ if [ -x "$(command -v singularity)" ]; then
-c src/nf_modules/rsem/quantification_single.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index*" \
- --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+ --fastq "data/tiny_dataset/fastq/tiny*_R1.fastq" \
-resume
./nextflow src/nf_modules/rsem/quantification_paired.nf \
--
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