Commit 234c9659 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Merge branch 'develop' into 'master'

Develop

See merge request !74
parents ab04237e 80ae9913
Pipeline #8278 passed with stages
in 11 minutes and 47 seconds
# v2.2.0
**UserFacing**
* Update cellranger to version 4.0.0
**Background**
* Add runtime info
* Make standard (profile) be biohpc AND cluster
*Known Bugs*
* cellranger mkfastq will not accept spaces in path for run param even if quoted, issue raised on 10XGenomics/cellranger github issue [#31](https://github.com/10XGenomics/cellranger/issues/31)
* note: 10x doesn't check github issues, emailed instead
* note: pipeline checks for spaces and exits prematurely if found
* If multiple flowcells (tar'd) files are inputted then there will be multiple fastq's by the same name, currently dealing with that name conflict is not tractable
* note: if multiple bcl files are detected then cellranger_count design file is not created
* If too many (or too large) .tar(.gz) bcl files are placed in one run, aws runs appears to fail possibly due to timeout on staging
# v2.1.5
**UserFacing**
* Check Design File for spaces in name and file contents
......
......@@ -32,7 +32,7 @@ bclCount = Channel
.count()
// Define regular variables
pipelineVersion = "2.1.5"
pipelineVersion = "2.2.0"
name = params.name
designLocation = Channel
.fromPath(params.designFile)
......@@ -85,8 +85,26 @@ 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 +133,12 @@ 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'
......@@ -148,11 +164,10 @@ process untarBCL {
process mkfastq {
tag "${bcl.simpleName}"
publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}"
queue '128GB,256GB,256GBv1,384GB'
module 'cellranger/3.1.0:bcl2fastq/2.19.1'
module 'cellranger/4.0.0:bcl2fastq/2.19.1'
input:
file versions_cellrangerScript
......@@ -173,21 +188,18 @@ process mkfastq {
hostname
ulimit -u 16384
ulimit -a
cellranger mkfastq --id=mkfastq_${bcl.simpleName} --run=${bcl} --csv=${design} --ignore-dual-index ${mask}
cellranger mkfastq --id=mkfastq_${bcl.simpleName} --run=${bcl} --csv=${design} ${mask}
mkdir fq
mkdir "fq/${bcl.simpleName}"
find . -name "*.fastq.gz" -exec cp {} fq/${bcl.simpleName}/ \\;
bash versions_cellranger.sh > version_cellranger.txt
bash versions_bcl2fastq.sh > version_bcl2fastq.txt
"""
}
if (bclCount.value == 1) {
process countDesign {
tag "${name}"
publishDir "${outDir}/${task.process}/${name}", mode: 'copy'
......@@ -205,14 +217,11 @@ if (bclCount.value == 1) {
ulimit -a
bash countDesign.sh
"""
}
}
process fastqc {
tag "${bcl}"
module 'fastqc/0.11.5:parallel'
......@@ -235,12 +244,10 @@ 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 +273,10 @@ 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 +298,4 @@ process multiqc {
#export LANG=C.UTF-8
multiqc -c ${multiqcConf} .
"""
}
profiles {
standard {
includeConfig 'configs/biohpc.config'
includeConfig 'configs/cluster.config'
}
biohpc {
includeConfig 'configs/biohpc.config'
......@@ -47,6 +48,6 @@ manifest {
homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq'
description = 'This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illuminas bcl2fastq). It takes bcls and demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.'
mainScript = 'main.nf'
version = '2.1.5'
version = '2.2.0'
nextflowVersion = '>=0.31.0'
}
#!/usr/bin/env python
#!/usr/bin/env python3
#generate_references.py
#*
#* --------------------------------------------------------------------------
......
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