Commit 8798d60f authored by Gervaise Henry's avatar Gervaise Henry 🤠

Add runtime info

parent 7c71bf3c
......@@ -85,8 +85,25 @@ process trackStart {
}
process checkDesignFile {
log.info """\
BICF cellranger_mkfastq Pipeline
================================
Run name : ${params.name}
bcl : ${params.bcl}
Design File : ${params.designFile}
Output Directory: ${params.outDir}
--------------------------------
Nextflow Version: ${workflow.nextflow.version}
Pipeline Version: ${pipelineVersion}
Session ID : ${workflow.sessionId}
--------------------------------
Astrocyte : ${params.astrocyte}
CI : ${params.ci}
Development : ${params.dev}
"""
process checkDesignFile {
tag "${name}"
module 'python/3.6.1-2-anaconda'
......@@ -115,14 +132,12 @@ process checkDesignFile {
echo "${workflow.nextflow.version}" > version_nextflow.txt
echo "${pipelineVersion}" > version_pipeline.txt
"""
}
/* nextflow workflow manifest version calls that aren't compatible with Asrcocyte
echo "${workflow.manifest.version}" > version_pipeline.txt
*/
process untarBCL {
tag "${tar.simpleName}"
module 'pigz/2.4'
......@@ -148,7 +163,6 @@ process untarBCL {
process mkfastq {
tag "${bcl.simpleName}"
publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}"
queue '128GB,256GB,256GBv1,384GB'
......@@ -180,14 +194,11 @@ process mkfastq {
bash versions_cellranger.sh > version_cellranger.txt
bash versions_bcl2fastq.sh > version_bcl2fastq.txt
"""
}
if (bclCount.value == 1) {
process countDesign {
tag "${name}"
publishDir "${outDir}/${task.process}/${name}", mode: 'copy'
......@@ -205,14 +216,11 @@ if (bclCount.value == 1) {
ulimit -a
bash countDesign.sh
"""
}
}
process fastqc {
tag "${bcl}"
module 'fastqc/0.11.5:parallel'
......@@ -235,12 +243,10 @@ process fastqc {
bash fastqc.sh
bash versions_fastqc.sh > version_fastqc.txt
"""
}
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'
......@@ -266,12 +272,10 @@ process versions {
python3 generate_versions.py -f version_*.txt -o versions
python3 generate_references.py -r ${references} -o references
"""
}
process multiqc {
tag "${name}"
publishDir "${outDir}/${task.process}/${name}", mode: 'copy', pattern: "{multiqc*}"
module 'multiqc/1.7'
......@@ -293,5 +297,4 @@ process multiqc {
#export LANG=C.UTF-8
multiqc -c ${multiqcConf} .
"""
}
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