Merge branch '26-v3.1.0' into 'develop'

Resolve "Change to cellranger v 3.1.0"

Closes #26 and #27

See merge request !42

.gitlab-ci.yml

@@ -35,6 +35,7 @@ simple_1FC:
     when: always
     paths:
       - .nextflow.log
+      - workflow/output/multiqc/run/multiqc_report.html
     expire_in: 2 days
   retry:
     max: 1
@@ -51,6 +52,7 @@ simple_2FC:
     when: always
     paths:
       - .nextflow.log
+      - workflow/output/multiqc/run/multiqc_report.html
     expire_in: 2 days
   retry:
     max: 1

CHANGELOG.md

 # v1.3.0 (in development)
 **User Facing**
+* Change Cellranger Version to 3.1.0
+* Add CI artifacts
 
 **Background**
 

astrocyte_pkg.yml

@@ -40,7 +40,7 @@ documentation_files:
 # Specify versioned module names to ensure reproducability.
 workflow_modules:
   - 'python/3.6.1-2-anaconda'
-  - 'cellranger/2.1.1'
+  - 'cellranger/3.1.0'
   - 'bcl2fastq/2.17.1.14'
   - 'fastqc/0.11.5'
   - 'parallel'

workflow/conf/biohpc.config

@@ -12,7 +12,7 @@ process {
     queue = 'super'
   }
   withLabel:mkfastq {
-    module = ['cellranger/3.0.2', 'bcl2fastq/2.19.1']
+    module = ['cellranger/3.1.0', 'bcl2fastq/2.19.1']
     queue = '128GB,256GB,256GBv1,384GB'
   }
   withLabel:fastqc {

workflow/main.nf

@@ -81,7 +81,7 @@ process mkfastq {
   tag "${bcl.baseName}"
   queue '128GB,256GB,256GBv1,384GB'
   publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}"
-  module 'cellranger/3.0.2:bcl2fastq/2.19.1'
+  module 'cellranger/3.1.0:bcl2fastq/2.19.1'
 
   input:
     each bcl from bclPaths.collect()
@@ -156,7 +156,7 @@ process versions {
 
   tag "${name}"
   publishDir "${outDir}/misc/${task.process}/${name}", mode: 'copy'
-  module 'python/3.6.1-2-anaconda:cellranger/3.0.2:bcl2fastq/2.19.1:fastqc/0.11.5:pandoc/2.7'
+  module 'python/3.6.1-2-anaconda:cellranger/3.1.0:bcl2fastq/2.19.1:fastqc/0.11.5:pandoc/2.7'
 
   input: