Commit d5871e2a authored by Gervaise Henry's avatar Gervaise Henry 🤠

Merge branch 'containerize' into 'cellranger-4.0.0_ref-2020A'

# Conflicts:
#   workflow/main.nf
#   workflow/nextflow.config
parents 7838ab2c 7dc9041e
Pipeline #8250 passed with stages
in 13 minutes and 34 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"
"""
}
*/
log.info """\
================================
......@@ -106,7 +107,6 @@ Development : ${params.dev}
process checkDesignFile {
tag "${name}"
module 'python/3.6.1-2-anaconda'
input:
file check_designScript
......@@ -140,7 +140,6 @@ process checkDesignFile {
process untarBCL {
tag "${tar.simpleName}"
module 'pigz/2.4'
input:
file untarBCLScript
......@@ -167,7 +166,6 @@ process mkfastq {
tag "${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
......@@ -223,7 +221,6 @@ if (bclCount.value == 1) {
process fastqc {
tag "${bcl}"
module 'fastqc/0.11.5:parallel'
input:
file fastqcScript
......@@ -249,7 +246,6 @@ process fastqc {
process versions {
tag "${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
......@@ -279,7 +275,6 @@ process versions {
process multiqc {
tag "${name}"
publishDir "${outDir}/${task.process}/${name}", mode: 'copy', pattern: "{multiqc*}"
module 'multiqc/1.7'
input:
file multiqcConf
......
......@@ -23,6 +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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