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BICF
Astrocyte
cellranger_mkfastq
Commits
60166999
Commit
60166999
authored
Jul 17, 2020
by
Gervaise Henry
🤠
Browse files
recontaineraize
parent
4a6e4222
Pipeline
#7601
passed with stages
in 5 minutes and 54 seconds
Changes
3
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
workflow/configs/biohpc.config
View file @
60166999
...
...
@@ -3,3 +3,7 @@ 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 @
60166999
...
...
@@ -63,6 +63,7 @@ references = Channel.fromPath("${baseDir}/../docs/references.md")
*/
params.ci = false
params.dev = false
/*
process trackStart {
script:
"""
...
...
@@ -83,7 +84,7 @@ process trackStart {
"https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
"""
}
*/
process checkDesignFile {
...
...
workflow/nextflow.config
View file @
60166999
profiles
{
standard
{
includeConfig
'configs/biohpc.config'
includeConfig
'configs/cluster.config'
}
biohpc
{
includeConfig
'configs/biohpc.config'
...
...
@@ -22,6 +23,34 @@ 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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