Add in paired end test and switch organisms.

.gitlab-ci.yml

@@ -23,6 +23,6 @@ single_end_mouse:
 paired_end_human:
   stage: integration
   script:
-  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true
+  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR451NAE_PE.txt" --genome 'GRCm38' --pairedEnd true
   artifacts:
     expire_in: 2 days

workflow/main.nf

@@ -9,7 +9,7 @@ params.pairedEnd = false
 params.chrM = true
 params.tn5 = true
 params.designFile = "$baseDir/../test_data/design_ENCSR265ZXX_SE.txt"
-params.genome = 'GRCm38'
+params.genome = 'GRCh38'
 params.genomes = []
 params.bwaIndex = params.genome ? params.genomes[ params.genome ].bwa ?: false : false
 params.genomeSize = params.genome ? params.genomes[ params.genome ].genomesize ?: false : false