Commit 60166999 authored by Gervaise Henry's avatar Gervaise Henry 🤠

recontaineraize

parent 4a6e4222
Pipeline #7601 passed with stages
in 5 minutes and 54 seconds
......@@ -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/'
}
......@@ -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 {
......
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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