Merge branch '35-fix-astrocyte' into 'master'

Move single-end to run on astrocyte.

Closes #35

See merge request !28

.gitlab-ci.yml

@@ -32,7 +32,7 @@ single_end_mouse:
   only:
     - master
   script:
-  - nextflow run workflow/main.nf --astrocyte 'false' -resume
+  - nextflow run workflow/main.nf --astrocyte 'true' -resume
   - pytest -m singleend
   artifacts:
     expire_in: 2 days

astrocyte_pkg.yml

@@ -108,7 +108,7 @@ workflow_parameters:
       end to the other, generating the sequence of base pairs. In paired-end
       reading it starts at one read, finishes this direction at the specified
       read length, and then starts another round of reading from the opposite
-      end of the fragment.
+      end of the fragment. (Paired-end: True, Single-end: False)
 
   - id: design
     type: file

workflow/main.nf

@@ -22,9 +22,9 @@ params.multiqc =  "$baseDir/conf/multiqc_config.yaml"
 if (params.astrocyte) {
   print("Running under astrocyte")
   referenceLocation = "/project/shared/bicf_workflow_ref"
-  params.bwaIndex = "$referenceLocation/$genome"
-  params.chromSizes = "$referenceLocation/$genome/genomefile.txt"
-  params.fasta = "$referenceLocation/$genome/genome.fa.txt"
+  params.bwaIndex = "$referenceLocation/$params.genome"
+  params.chromSizes = "$referenceLocation/$params.genome/genomefile.txt"
+  params.fasta = "$referenceLocation/$params.genome/genome.fa.txt"
   if (params.genome == 'GRCh37' || params.genome == 'GRCh38') {
     params.genomeSize = 'hs'
   } else if (params.chromSizes == 'GRCm38') {