Commit 6e722372 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Add basic multiqc process

parent c6bfd08e
Pipeline #3431 passed with stages
in 1 minute and 10 seconds
|*master*|*develop*|
|:-:|:-:|
|[![Build Status](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/badges/master/build.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/commits/master)|[![Build Status](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/badges/develop/build.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/commits/develop)|
10x Genomics scRNA-Seq (cellranger) mkfastq Pipeline
========================================
......
......@@ -15,6 +15,9 @@ process {
module = ['cellranger/3.0.2', 'bcl2fastq/2.19.1']
queue = '128GB,256GB,256GBv1,384GB'
}
withLabel: multiqc {
module = ['multiqc/1.7']
}
}
......
......@@ -67,7 +67,6 @@ process untarBCL {
"""
}
process mkfastq {
tag "${bcl.baseName}"
queue '128GB,256GB,256GBv1,384GB'
......@@ -82,6 +81,7 @@ process mkfastq {
output:
file("**/outs/fastq_path/**/*") into fastqPaths
file("**/outs/fastq_path/Stats/Stats.json") into qc
script:
......@@ -93,3 +93,24 @@ process mkfastq {
cellranger mkfastq --id="${bcl.baseName}" --run=$bcl --csv=$designPaths -r \$SLURM_CPUS_ON_NODE -p \$SLURM_CPUS_ON_NODE -w \$SLURM_CPUS_ON_NODE
"""
}
process multiqc {
publishDir "$outDir/${task.process}", mode: 'copy'
input:
file qc
output:
file("*") into qcPaths
script:
"""
hostname
ulimit -a
module load multiqc/1.7
multiqc Stats.json
"""
}
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