Commit 92f1396c authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Merge branch 'develop' into 'master'

Fix multi sample, local ulimit set, v2.1.1

See merge request !74
parents e913ede6 079739df
Pipeline #7406 passed with stages
in 17 minutes and 40 seconds
# v2.1.0
# v2.1.1
**User Facing**
* Check Design File for spaces in name and file contents
* Attempt to prevent thredding error (which appears to only happen on 256GBv1 nodes)
......
......@@ -33,7 +33,7 @@ params.outDir = "${baseDir}/output"
// Variable error test
if (params.kitVersion == "3GEXv3" && params.version == '2.1.1') {
print("Cellranger Version 2.1.1 requires kitVersion 2")
System.exit(32)
System.exit(1)
}
// Define variables if astrocyte (or from config)
......@@ -60,7 +60,7 @@ if (params.astrocyte) {
params.genomeLocationFull = params.genomeLocation+params.genome
// Define variables from input
pipelineVersion = "2.1.0"
pipelineVersion = "2.1.1"
name = params.name
designLocation = Channel
.fromPath(params.designFile)
......@@ -99,7 +99,6 @@ process trackStart {
script:
"""
hostname
ulimit -u 16384
ulimit -a
export https_proxy=\${http_proxy}
......@@ -135,7 +134,6 @@ process checkDesignFile {
script:
"""
hostname
ulimit -u 16384
ulimit -a
noSpaceDesign=\$(echo "${designLocation}" | tr -d ' ')
if [[ "\${noSpaceDesign}" != "${designLocation}" ]]; then
......@@ -151,9 +149,11 @@ samples = designPaths
.splitCsv (sep: ',', header: true)
.map { row -> [ row.Sample, file(row.fastq_R1), file(row.fastq_R2) ] }
.groupTuple()
.combine(filename_checkScript)
//.subscribe { println it }
// Duplicate variables
samples.into {
samples211
samples302
......@@ -173,11 +173,6 @@ forceCells310 = forceCells
chemistryParam211 = chemistryParam
chemistryParam302 = chemistryParam
chemistryParam310 = chemistryParam
filename_checkScript.into {
filename_checkScript211
filename_checkScript302
filename_checkScript310
}
/*
......@@ -190,12 +185,11 @@ process count211 {
module 'cellranger/2.1.1'
input:
set sample, file("${sample}_S1_L00?_R1_001.fastq.gz"), file("${sample}_S1_L00?_R2_001.fastq.gz") from samples211
set sample, file("${sample}_S?_L001_R1_001.fastq.gz"), file("${sample}_S?_L001_R2_001.fastq.gz"), file(script) from samples211
file ref from refLocation211.first()
expectCells211
forceCells211
chemistryParam211
file filename_checkScript211
output:
file("**/outs/**") into outPaths211
......@@ -238,12 +232,11 @@ process count302 {
module 'cellranger/3.0.2'
input:
set sample, file("${sample}_S?_L001_R1_001.fastq.gz"), file("${sample}_S?_L001_R2_001.fastq.gz") from samples302
set sample, file("${sample}_S?_L001_R1_001.fastq.gz"), file("${sample}_S?_L001_R2_001.fastq.gz"), file(script) from samples302
file ref from refLocation302.first()
expectCells302
forceCells302
chemistryParam302
file filename_checkScript302
output:
file("**/outs/**") into outPaths302
......@@ -285,12 +278,11 @@ process count310 {
module 'cellranger/3.1.0'
input:
set sample, file("${sample}_S?_L001_R1_001.fastq.gz"), file("${sample}_S?_L001_R2_001.fastq.gz") from samples310
set sample, file("${sample}_S?_L001_R1_001.fastq.gz"), file("${sample}_S?_L001_R2_001.fastq.gz"), file(script) from samples310
file ref from refLocation310.first()
expectCells310
forceCells310
chemistryParam310
file filename_checkScript310
output:
file("**/outs/**") into outPaths310
......@@ -340,7 +332,6 @@ process versions {
script:
"""
hostname
ulimit -u 16384
ulimit -a
echo "${workflow.nextflow.version}" > version_nextflow.txt
echo "${pipelineVersion}" > version_pipeline.txt
......@@ -372,7 +363,6 @@ process multiqc {
script:
"""
hostname
ulimit -u 16384
ulimit -a
awk 'FNR==1 && NR!=1{next;}{print}' *.tsv > metrics_summary_mqc.tsv
sed -i '1s/^.*\tE/Sample\tE/' metrics_summary_mqc.tsv
......
......@@ -47,6 +47,6 @@ manifest {
homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count'
description = 'This pipeline is a wrapper for the cellranger count tool from 10x Genomics. It takes fastq files from 10x Genomics Single Cell Gene Expression libraries, performs alignment, filtering, barcode counting, and UMI counting. It uses the Chromium cellular barcodes to generate gene-barcode matrices, determine clusters, and perform gene expression analysis.'
mainScript = 'main.nf'
version = '2.1.0'
version = '2.1.1'
nextflowVersion = '>=0.31.0'
}
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment