Commit ab04237e authored by Gervaise Henry's avatar Gervaise Henry 🤠

Merge branch 'develop' into 'master'

Fix local process ulimit set

See merge request !69
parents b118149f 4a6e4222
Pipeline #7404 passed with stages
in 340 minutes and 3 seconds
# v2.1.4 # v2.1.5
**UserFacing** **UserFacing**
* Check Design File for spaces in name and file contents * Check Design File for spaces in name and file contents
* Update design example, README, and astrocyte.yml with current barcode IDs * Update design example, README, and astrocyte.yml with current barcode IDs
......
...@@ -32,7 +32,7 @@ bclCount = Channel ...@@ -32,7 +32,7 @@ bclCount = Channel
.count() .count()
// Define regular variables // Define regular variables
pipelineVersion = "2.1.4" pipelineVersion = "2.1.5"
name = params.name name = params.name
designLocation = Channel designLocation = Channel
.fromPath(params.designFile) .fromPath(params.designFile)
...@@ -105,7 +105,6 @@ process checkDesignFile { ...@@ -105,7 +105,6 @@ process checkDesignFile {
script: script:
""" """
hostname hostname
ulimit -u 16384
ulimit -a ulimit -a
noSpaceDesign=\$(echo "${designLocation}" | tr -d ' ') noSpaceDesign=\$(echo "${designLocation}" | tr -d ' ')
if [[ "\${noSpaceDesign}" != "${designLocation}" ]]; then if [[ "\${noSpaceDesign}" != "${designLocation}" ]]; then
...@@ -203,7 +202,6 @@ if (bclCount.value == 1) { ...@@ -203,7 +202,6 @@ if (bclCount.value == 1) {
script: script:
""" """
hostname hostname
ulimit -u 16384
ulimit -a ulimit -a
bash countDesign.sh bash countDesign.sh
""" """
...@@ -264,7 +262,6 @@ process versions { ...@@ -264,7 +262,6 @@ process versions {
script: script:
""" """
hostname hostname
ulimit -u 16384
ulimit -a ulimit -a
python3 generate_versions.py -f version_*.txt -o versions python3 generate_versions.py -f version_*.txt -o versions
python3 generate_references.py -r ${references} -o references python3 generate_references.py -r ${references} -o references
...@@ -291,7 +288,6 @@ process multiqc { ...@@ -291,7 +288,6 @@ process multiqc {
script: script:
""" """
hostname hostname
ulimit -u 16384
ulimit -a ulimit -a
#export LC_ALL=C.UTF-8 #export LC_ALL=C.UTF-8
#export LANG=C.UTF-8 #export LANG=C.UTF-8
......
...@@ -47,6 +47,6 @@ manifest { ...@@ -47,6 +47,6 @@ manifest {
homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq' homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq'
description = 'This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illuminas bcl2fastq). It takes bcls and demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.' description = 'This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illuminas bcl2fastq). It takes bcls and demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.'
mainScript = 'main.nf' mainScript = 'main.nf'
version = '2.1.4' version = '2.1.5'
nextflowVersion = '>=0.31.0' nextflowVersion = '>=0.31.0'
} }
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