Skip to content
Snippets Groups Projects
Commit b3b37b7e authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
Browse files

Revert "Test count211 for right cellranger module load"

This reverts commit 798c71d5
parent 798c71d5
Branches
Tags
4 merge requests!53Develop,!51Resolve "Add pytest to CI",!50Resolve "Add pytest to CI",!49Resolve "Add pytest to CI"
Pipeline #4477 canceled with stages
in 2 minutes and 48 seconds
......@@ -137,7 +137,6 @@ process count211 {
"""
hostname
ulimit -a
module list
bash ${baseDir}/scripts/filename_check.sh -r ${ref}
cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --expect-cells=${expectCells211}
sed -E 's/("([^"]*)")?,/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
......@@ -147,7 +146,6 @@ process count211 {
"""
hostname
ulimit -a
module list
bash ${baseDir}/scripts/filename_check.sh -r ${ref}
cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --force-cells=${forceCells211}
sed -E 's/("([^"]*)")?,/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment