Commit 0bdf504a authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Remove containers and add modules

parent fbf1a9f7
Pipeline #7348 failed with stages
in 13 minutes and 51 seconds
......@@ -78,6 +78,7 @@ process trackStart {
process checkDesignFile {
tag "${name}"
module 'python/3.6.1-2-anaconda'
input:
file check_designScript
......@@ -114,6 +115,7 @@ process checkDesignFile {
process untarBCL {
tag "${tar.simpleName}"
module 'pigz/2.4'
input:
file untarBCLScript
......@@ -140,6 +142,7 @@ process mkfastq {
tag "${bcl.simpleName}"
publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}"
module 'cellranger/3.1.0:bcl2fastq/2.19.1'
input:
file versions_cellrangerScript
......@@ -202,6 +205,7 @@ if (bclCount.value == 1) {
process fastqc {
tag "${bcl}"
module 'fastqc/0.11.5:parallel'
input:
file fastqcScript
......@@ -229,6 +233,7 @@ process fastqc {
process versions {
tag "${name}"
module 'python/3.6.1-2-anaconda:cellranger/3.1.0:bcl2fastq/2.19.1:fastqc/0.11.5:pandoc/2.7'
input:
file versionsScript
......@@ -261,6 +266,7 @@ process multiqc {
tag "${name}"
publishDir "${outDir}/${task.process}/${name}", mode: 'copy', pattern: "{multiqc*}"
module 'multiqc/1.7'
input:
file multiqcConf
......
......@@ -22,32 +22,6 @@ 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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