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BICF
Astrocyte
cellranger_count
Commits
7106c0a3
There was a problem fetching the pipeline stages.
Commit
7106c0a3
authored
5 years ago
by
Gervaise Henry
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Merge branch 'master' into 'develop'
# Conflicts: # astrocyte_pkg.yml
parents
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4 merge requests
!29
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!26
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!25
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Develop
Pipeline
#3315
passed with stages
in 10 minutes and 37 seconds
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4
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2
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.gitignore
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.gitignore
data/.gitkeep
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data/.gitkeep
workflow/conf/biohpc.config
+3
-3
3 additions, 3 deletions
workflow/conf/biohpc.config
workflow/main.nf
+17
-3
17 additions, 3 deletions
workflow/main.nf
with
21 additions
and
6 deletions
.gitignore
+
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−
0
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7106c0a3
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@@ -301,6 +301,7 @@ $RECYCLE.BIN/
/workflow/work/*
/workflow/output/*
/.nextflow/*
/data/*
/work/*
/output/*
pipeline_trace*.txt*
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data/.gitkeep
0 → 100644
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−
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workflow/conf/biohpc.config
+
3
−
3
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7106c0a3
...
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@@ -9,15 +9,15 @@ process {
}
$
count211
{
module
= [
'cellranger/2.1.1'
]
memory
=
'120
GB'
queue
=
'128GB,256GB,256GBv1,384
GB'
}
$
count301
{
module
= [
'cellranger/3.0.1'
]
memory
=
'120
GB'
queue
=
'128GB,256GB,256GBv1,384
GB'
}
$
count302
{
module
= [
'cellranger/3.0.2'
]
memory
=
'120
GB'
queue
=
'128GB,256GB,256GBv1,384
GB'
}
}
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workflow/main.nf
+
17
−
3
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7106c0a3
...
...
@@ -73,6 +73,8 @@ process checkDesignFile {
script:
"""
hostname
ulimit -a
module load python/3.6.1-2-anaconda
python3 $baseDir/scripts/check_design.py -d $designLocation -f $fastqList
"""
...
...
@@ -106,7 +108,7 @@ chemistryParam301 = chemistryParam
chemistryParam302 = chemistryParam
process count211 {
memory '120
GB'
queue '128GB,256GB,256GBv1,384
GB'
tag "count211-$sample"
publishDir "$outDir/${task.process}", mode: 'copy'
...
...
@@ -131,17 +133,21 @@ process count211 {
"""
if (forceCells211 == 0){
"""
hostname
ulimit -a
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells211
"""
} else {
"""
hostname
ulimit -a
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells211
"""
}
}
process count301 {
memory '120
GB'
queue '128GB,256GB,256GBv1,384
GB'
tag "count301-$sample"
publishDir "$outDir/${task.process}", mode: 'copy'
...
...
@@ -167,17 +173,21 @@ process count301 {
"""
if (forceCells301 == 0){
"""
hostname
ulimit -a
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells301 --chemistry="$chemistryParam301"
"""
} else {
"""
hostname
ulimit -a
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells301 --chemistry="$chemistryParam301"
"""
}
}
process count302 {
memory '120
GB'
queue '128GB,256GB,256GBv1,384
GB'
tag "count302-$sample"
publishDir "$outDir/${task.process}", mode: 'copy'
...
...
@@ -203,10 +213,14 @@ process count302 {
"""
if (forceCells302 == 0){
"""
hostname
ulimit -a
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells302 --chemistry="$chemistryParam302"
"""
} else {
"""
hostname
ulimit -a
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells302 --chemistry="$chemistryParam302"
"""
}
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