Fix track pipeline.

.gitlab-ci.yml

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

workflow/main.nf

@@ -20,6 +20,7 @@ params.astrocyte = false
 params.outDir= "${baseDir}/output"
 params.references = "${baseDir}/../docs/references.md"
 params.multiqc =  "${baseDir}/conf/multiqc_config.yaml"
+params.ci = false
 
 // Check inputs
 if(params.bwaIndex) {
@@ -54,7 +55,7 @@ geneNames = params.geneNames
 /*
  * trackStart: track start of pipeline
  */
-params.ci = false
+
 process trackStart {
   script:
   """
@@ -64,12 +65,12 @@ process trackStart {
 
   curl -H 'Content-Type: application/json' -X PUT -d '{ \
       "sessionId": "${workflow.sessionId}", \
-      "pipeline": "${workflow.manifest.name}", \
+      "pipeline": "atacseq_analysis", \
       "start": "${workflow.start}", \
       "astrocyte": ${params.astrocyte}, \
       "status": "started", \
-      "nextflowVersion": "${workflow.nextflow.version}",
-      "pipelineVersion": "${workflow.manifest.version}",
+      "nextflowVersion": "${workflow.nextflow.version}", \
+      "pipelineVersion": "2.0.0", \
       "ci": ${params.ci}}' \
   "https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
   """