Update changelog

CHANGELOG.md

@@ -4,6 +4,10 @@
 * 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
+* Add parameter for base mask (not available in Astrocyte)
+* Output Nextflow version in QC report
+* Output pipeline version (manual) in QC report
 
 **Background**
 * Add Nextflow Tower integration into CI (GHH's profile)

docs/index.md

@@ -4,7 +4,7 @@
 Introduction
 ------------
 
-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.
+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.
 
 FastQC is run on the resulting fastq and those reports and bcl2fastq reports are collated with the MultiQC tool.
 
@@ -29,8 +29,8 @@ To Run:
 
 * Design example:
 
-    | Lane | Sample      | Index     |
-    |------|-------------|-----------|
+    | Lane | Sample      | Index    |
+    |------|-------------|----------|
     | *    | test_sample | SI-GA-C9 |
     
 

workflow/nextflow.config

@@ -36,7 +36,7 @@ tower {
 
 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.'
+  description = 'This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illuminas bcl2fastq). It takes bcl's and demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.'
   mainScript = 'main.nf'
   version = '2.0.0-indev'
   nextflowVersion = '>=0.31.0'