Merge branch 'develop' into 'master'

Develop

See merge request !68

CHANGELOG.md

-# v2.1.3
+# v2.1.4
 **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.
 
@@ -48,19 +48,22 @@ To Run:
     * run name, puts outputs in a directory with this name
     * eg: **--name 'test'**
   * **--bcl**
-    * Base call files (tarballed [*.tar] +/- gunzipping [*.tar.gz] from a sequencing of 10x single-cell expereiment, supports pigr parallelization).
-    * There can be multiple basecall files, but they all will be demultiplexed by the same design file.
+    * base call files (tarballed [*.tar] +/- gunzipping [*.tar.gz] from a sequencing of 10x single-cell expereiment, supports pigr parallelization)
+    * there can be multiple basecall files, but they all will be demultiplexed by the same design file
     * eg: ```--bcl '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-1_2_0.tar.gz'```
   * **--designFile**
     * path to design file (csv format) location
     * column 1 = "Lane" (number of lanes to demultiplex, **\*** for all lanes)
     * column 2 = "Sample" (sample name)
     * column 3 = "Index" (10x sample index barcode, eg SI-GA-A1)
-    * Last character set in Index references the well position of the 96-well plate that the sample barcode kit is sold in.
+    * last character set in Index references the well position of the 96-well plate that the sample barcode kit is sold in
     * [Current sample barcode IDs](https://s3-us-west-2.amazonaws.com/10x.files/supp/cell-exp/chromium-shared-sample-indexes-plate.csv)
     * can have repeated "Sample" if there are multiple fastq R1/R2 pairs for the samples
     * can be downloaded [HERE](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/master/docs/design.csv)
     * eg: ```--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple/cellranger-tiny-bcl-simple-1_2_0.csv'```
+  * **--mask**
+    * add a base mask if the sequencing strategy doesn't match the requirements of 10x Genomics
+    * eg: **--mask '--use-bases-mask=Y\*,I8n\*,n\*,Y\*'**
   * **--outDir**
     * optional output directory for run
     * eg: ```--outDir 'test'```
@@ -70,8 +73,8 @@ To Run:
   ```
 * Design example:
 
-| Lane | Sample      | Index     |
-|------|-------------|-----------|
+| Lane | Sample      | Index    |
+|------|-------------|----------|
 | *    | test_sample | SI-GA-C9 |
 
 

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"
 
@@ -31,11 +32,12 @@ bclCount = Channel
   .count()
 
 // Define regular variables
-pipelineVersion = "2.1.3"
+pipelineVersion = "2.1.4"
 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 = '2.1.4'
   nextflowVersion = '>=0.31.0'
 }