Fix pipeline.

.gitlab-ci.yml

@@ -30,7 +30,7 @@ single_end_human:
     - branches
     - master
   script:
-  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --ci true
+  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --ci true --dev true
   - pytest -m singleend_human
 
 
@@ -40,5 +40,5 @@ paired_end_mouse:
     - branches
     - master
   script:
-  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR451NAE_PE.txt" --genome 'GRCm38' --pairedEnd true --blacklist true --astrocyte true --ci true
+  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR451NAE_PE.txt" --genome 'GRCm38' --pairedEnd true --blacklist true --astrocyte true --ci true --dev true
   - pytest -m pairedend_mouse

workflow/main.nf

@@ -21,6 +21,7 @@ params.outDir= "${baseDir}/output"
 params.references = "${baseDir}/../docs/references.md"
 params.multiqc =  "${baseDir}/conf/multiqc_config.yaml"
 params.ci = false
+params.dev = false
 
 // Check inputs
 if(params.bwaIndex) {
@@ -71,7 +72,8 @@ process trackStart {
       "status": "started", \
       "nextflowVersion": "${workflow.nextflow.version}", \
       "pipelineVersion": "2.0.0", \
-      "ci": ${params.ci}}' \
+      "ci": '${params.ci}}' \
+      "dev": '${params.dev}}' \
   "https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
   """
 }