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cellranger_mkfastq
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BICF
Astrocyte
cellranger_mkfastq
Commits
acd28db3
Commit
acd28db3
authored
Oct 30, 2020
by
Gervaise Henry
🤠
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Revert "Merge branch 'containerize' into 'cellranger-4.0.0_ref-2020A'"
This reverts commit
d5871e2a
parent
d5871e2a
Pipeline
#8251
passed with stages
in 13 minutes and 7 seconds
Changes
3
Pipelines
1
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3 changed files
with
7 additions
and
34 deletions
+7
-34
workflow/configs/biohpc.config
workflow/configs/biohpc.config
+0
-4
workflow/main.nf
workflow/main.nf
+7
-2
workflow/nextflow.config
workflow/nextflow.config
+0
-28
No files found.
workflow/configs/biohpc.config
View file @
acd28db3
...
...
@@ -3,7 +3,3 @@ env {
https_proxy
=
'http://proxy.swmed.edu:3128'
all_proxy
=
'http://proxy.swmed.edu:3128'
}
singularity
{
cacheDir
=
'/project/shared/bicf_workflow_ref/singularity_images/'
}
workflow/main.nf
View file @
acd28db3
...
...
@@ -63,7 +63,6 @@ references = Channel.fromPath("${baseDir}/../docs/references.md")
*/
params.ci = false
params.dev = false
/*
process trackStart {
script:
"""
...
...
@@ -84,7 +83,7 @@ process trackStart {
"https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
"""
}
*/
log.info """\
================================
...
...
@@ -107,6 +106,7 @@ Development : ${params.dev}
process checkDesignFile {
tag "${name}"
module 'python/3.6.1-2-anaconda'
input:
file check_designScript
...
...
@@ -140,6 +140,7 @@ process checkDesignFile {
process untarBCL {
tag "${tar.simpleName}"
module 'pigz/2.4'
input:
file untarBCLScript
...
...
@@ -166,6 +167,7 @@ process mkfastq {
tag "${bcl.simpleName}"
publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}"
queue '128GB,256GB,256GBv1,384GB'
module 'cellranger/4.0.0:bcl2fastq/2.19.1'
input:
file versions_cellrangerScript
...
...
@@ -221,6 +223,7 @@ if (bclCount.value == 1) {
process fastqc {
tag "${bcl}"
module 'fastqc/0.11.5:parallel'
input:
file fastqcScript
...
...
@@ -246,6 +249,7 @@ process fastqc {
process versions {
tag "${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
...
...
@@ -275,6 +279,7 @@ process versions {
process multiqc {
tag "${name}"
publishDir "${outDir}/${task.process}/${name}", mode: 'copy', pattern: "{multiqc*}"
module 'multiqc/1.7'
input:
file multiqcConf
...
...
workflow/nextflow.config
View file @
acd28db3
...
...
@@ -23,34 +23,6 @@ profiles {
}
}
process
{
withName
:
trackStart
{
container
=
'docker://bicf/bicfbase:2.0.0'
}
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
}
trace
{
enabled
=
true
file
=
'pipeline_trace.txt'
...
...
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