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cellranger_mkfastq
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BICF
Astrocyte
cellranger_mkfastq
Commits
ab04237e
Commit
ab04237e
authored
Jun 21, 2020
by
Gervaise Henry
🤠
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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
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CHANGELOG.md
CHANGELOG.md
+1
-1
workflow/main.nf
workflow/main.nf
+1
-5
workflow/nextflow.config
workflow/nextflow.config
+1
-1
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CHANGELOG.md
View file @
ab04237e
# v2.1.
4
# v2.1.
5
**UserFacing**
*
Check Design File for spaces in name and file contents
*
Update design example, README, and astrocyte.yml with current barcode IDs
...
...
workflow/main.nf
View file @
ab04237e
...
...
@@ -32,7 +32,7 @@ bclCount = Channel
.count()
// Define regular variables
pipelineVersion = "2.1.
4
"
pipelineVersion = "2.1.
5
"
name = params.name
designLocation = Channel
.fromPath(params.designFile)
...
...
@@ -105,7 +105,6 @@ process checkDesignFile {
script:
"""
hostname
ulimit -u 16384
ulimit -a
noSpaceDesign=\$(echo "${designLocation}" | tr -d ' ')
if [[ "\${noSpaceDesign}" != "${designLocation}" ]]; then
...
...
@@ -203,7 +202,6 @@ if (bclCount.value == 1) {
script:
"""
hostname
ulimit -u 16384
ulimit -a
bash countDesign.sh
"""
...
...
@@ -264,7 +262,6 @@ process versions {
script:
"""
hostname
ulimit -u 16384
ulimit -a
python3 generate_versions.py -f version_*.txt -o versions
python3 generate_references.py -r ${references} -o references
...
...
@@ -291,7 +288,6 @@ process multiqc {
script:
"""
hostname
ulimit -u 16384
ulimit -a
#export LC_ALL=C.UTF-8
#export LANG=C.UTF-8
...
...
workflow/nextflow.config
View file @
ab04237e
...
...
@@ -47,6 +47,6 @@ manifest {
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.'
mainScript
=
'main.nf'
version
=
'2.1.
4
'
version
=
'2.1.
5
'
nextflowVersion
=
'>=0.31.0'
}
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