Commit 9f942c94 authored by Gervaise Henry's avatar Gervaise Henry 🤠

Revert "Use base mask I1 = 8n, version 2.1.3"

This reverts commit 35c57522
parent 6a4c2aff
Pipeline #7373 passed with stages
in 7 minutes and 8 seconds
# v2.1.3
# v2.1.2
**UserFacing**
* Check Design File for spaces in name and file contents
* Update design example, README, and astrocyte.yml with current barcode IDs
* Remove unnecessary intermediate process files
* Add config option for running on AWS
* Ignore dual index
* Use base mask (I1 = 8n)
* Add parameter for base mask (not available in Astrocyte)
* Output Nextflow version in QC report
* Output pipeline version (manual) in QC report
......
......@@ -10,7 +10,7 @@
Introduction
------------
This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illumina's bcl2fastq). It takes bcl's and demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.
This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illumina's bcl2fastq). It takes demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.
FastQC is run on the resulting fastq and those reports and bcl2fastq reports are collated with the MultiQC tool.
......
......@@ -20,6 +20,7 @@ main.nf
params.name = "run"
params.bcl = "${baseDir}/../test_data/simple1/*.tar.gz"
params.designFile = "${baseDir}/../test_data/single1/cellranger-tiny-bcl-simple-1_2_0.csv"
params.mask = ""
params.astrocyte = false
params.outDir = "${baseDir}/output"
......@@ -36,6 +37,7 @@ name = params.name
designLocation = Channel
.fromPath(params.designFile)
.ifEmpty { exit 1, "design file not found: ${params.designFile}" }
mask = params.mask
outDir = params.outDir
// Define script files
......@@ -172,7 +174,7 @@ process mkfastq {
hostname
ulimit -u 16384
ulimit -a
cellranger mkfastq --id=mkfastq_${bcl.simpleName} --run=${bcl} --csv=${design} --ignore-dual-index --use-bases-mask=Y*,I8n*,n*,Y*
cellranger mkfastq --id=mkfastq_${bcl.simpleName} --run=${bcl} --csv=${design} --ignore-dual-index ${mask}
mkdir fq
mkdir "fq/${bcl.simpleName}"
find . -name "*.fastq.gz" -exec cp {} fq/${bcl.simpleName}/ \\;
......
......@@ -47,6 +47,6 @@ 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 = '2.1.3'
version = '2.1.2'
nextflowVersion = '>=0.31.0'
}
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