Merge branch 'revert-35c57522' into 'develop'

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

See merge request !67

CHANGELOG.md

-# 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
 

README.md

@@ -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.
 

workflow/main.nf

@@ -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}/ \\;

workflow/nextflow.config

@@ -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'
 }