Add pipeline tracking

workflow/main.nf

@@ -23,6 +23,7 @@ bclCount = Channel
   .count()
 
 // Define regular variables
+pipelineVersion = "2.x.x-indev"
 name = params.name
 designLocation = Channel
   .fromPath(params.designFile)
@@ -48,6 +49,31 @@ multiqcConf = Channel.fromPath("${baseDir}/configs/multiqc_config.yaml")
 references = Channel.fromPath("${baseDir}/../docs/references.md")
 
 
+/*
+ * trackStart: track start of pipeline
+ */
+params.ci = false
+process trackStart {
+  script:
+  """
+  hostname
+  ulimit -a
+  export https_proxy=\${http_proxy}
+ 
+  curl -H 'Content-Type: application/json' -X PUT -d '{ \
+      "sessionId": "${workflow.sessionId}", \
+      "pipeline": "cellranger_mkfastq", \
+      "pipelineVersion": "${pipelineVersion}", \
+      "start": "${workflow.start}", \
+      "astrocyte": ${params.astrocyte}, \
+      "status": "started", \
+      "nextflowVersion": "${workflow.nextflow.version}",
+      "ci": ${params.ci}}' \
+  "https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
+  """
+}
+
+
 process checkDesignFile {
 
   tag "${name}"
@@ -76,7 +102,7 @@ process checkDesignFile {
     python3 check_design.py -d \${noSpaceDesign}
     bash versions_python.sh > version_python.txt
     echo "${workflow.nextflow.version}" > version_nextflow.txt
-    echo "2.x.x-indev" > version_pipeline.txt
+    echo "${pipelineVersion" > version_pipeline.txt
     """
 
 }