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cellranger_mkfastq
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BICF
Astrocyte
cellranger_mkfastq
Commits
0bdf504a
Commit
0bdf504a
authored
4 years ago
by
Gervaise Henry
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Remove containers and add modules
parent
fbf1a9f7
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2 merge requests
!63
Develop
,
!62
De containerize
Pipeline
#7348
failed with stages
in 13 minutes and 51 seconds
Changes
2
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1
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2 changed files
workflow/main.nf
+6
-0
6 additions, 0 deletions
workflow/main.nf
workflow/nextflow.config
+0
-26
0 additions, 26 deletions
workflow/nextflow.config
with
6 additions
and
26 deletions
workflow/main.nf
+
6
−
0
View file @
0bdf504a
...
...
@@ -78,6 +78,7 @@ process trackStart {
process checkDesignFile {
tag "${name}"
module 'python/3.6.1-2-anaconda'
input:
file check_designScript
...
...
@@ -114,6 +115,7 @@ process checkDesignFile {
process untarBCL {
tag "${tar.simpleName}"
module 'pigz/2.4'
input:
file untarBCLScript
...
...
@@ -140,6 +142,7 @@ process mkfastq {
tag "${bcl.simpleName}"
publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}"
module 'cellranger/3.1.0:bcl2fastq/2.19.1'
input:
file versions_cellrangerScript
...
...
@@ -202,6 +205,7 @@ if (bclCount.value == 1) {
process fastqc {
tag "${bcl}"
module 'fastqc/0.11.5:parallel'
input:
file fastqcScript
...
...
@@ -229,6 +233,7 @@ process fastqc {
process versions {
tag "${name}"
module 'python/3.6.1-2-anaconda:cellranger/3.1.0:bcl2fastq/2.19.1:fastqc/0.11.5:pandoc/2.7'
input:
file versionsScript
...
...
@@ -261,6 +266,7 @@ process multiqc {
tag "${name}"
publishDir "${outDir}/${task.process}/${name}", mode: 'copy', pattern: "{multiqc*}"
module 'multiqc/1.7'
input:
file multiqcConf
...
...
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workflow/nextflow.config
+
0
−
26
View file @
0bdf504a
...
...
@@ -22,32 +22,6 @@ profiles {
}
}
process
{
withName
:
checkDesignFile
{
container
=
'docker://bicf/python3:2.0.0'
}
withName
:
untarBCL
{
container
=
'docker://bicf/bicfbase:2.0.0'
}
withName
:
mkfastq
{
container
=
'docker://bicf/cellranger3.1.0:2.0.0'
}
withName
:
fastqc
{
container
=
'docker://bicf/fastqc:2.0.0'
}
withName
:
versions
{
container
=
'docker://bicf/python3:2.0.0'
}
withName
:
multiqc
{
container
=
'docker://bicf/multiqc:2.0.0'
}
}
singularity
{
enabled
=
true
cacheDir
=
'/project/shared/bicf_workflow_ref/singularity_images/'
}
trace
{
enabled
=
true
file
=
'pipeline_trace.txt'
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