Version 2.1.4

CHANGELOG.md

-# v2.1.2
+# 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

README.md

@@ -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

@@ -32,7 +32,7 @@ bclCount = Channel
   .count()
 
 // Define regular variables
-pipelineVersion = "2.1.3"
+pipelineVersion = "2.1.4"
 name = params.name
 designLocation = Channel
   .fromPath(params.designFile)

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 = '2.1.2'
+  version = '2.1.4'
   nextflowVersion = '>=0.31.0'
 }