Commit 3bf48fd1 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Update containers to 2.0.0 and rejigger configs

parent 11e56b55
Pipeline #7342 passed with stages
in 6 minutes and 13 seconds
......@@ -14,24 +14,17 @@ process {
memory = '1 GB'
withName:checkDesignFile {
container = 'bicf/python3:1.3'
cpus = 4
}
withName:mkfastq {
container = 'bicf/cellranger3.1.0:1.0'
cpus = 6
memory = '2 GB'
}
withName:fastqc {
container = 'bicf/fastqc:1.5'
cpus = 30
memory = '15 GB'
}
withName:versions {
container = 'bicf/python3:1.3'
cpus = 6
}
withName:multiqc {
container = 'bicf/multiqc:1.4'
}
}
process {
container = 'docker://bicf/bicfbase:2.0.0'
withName:checkDesignFile {
container = 'docker://bicf/python3:1.3'
}
withName:mkfastq {
container = 'docker://bicf/cellranger3.1.0:1.0'
}
withName:fastqc {
container = 'docker://bicf/fastqc:1.5'
}
withName:versions {
container = 'docker://bicf/python3:1.3'
}
withName:multiqc {
container = 'docker://bicf/multiqc:1.4'
}
}
singularity {
enabled = true
cacheDir = '/project/shared/bicf_workflow_ref/singularity_images/'
}
env {
http_proxy = 'http://proxy.swmed.edu:3128'
https_proxy = 'http://proxy.swmed.edu:3128'
......
......@@ -22,6 +22,32 @@ 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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