Change pipeline tracking to curl

workflow/conf/biohpc.config

@@ -3,6 +3,9 @@ process {
   queue = 'super'
   clusterOptions = '--hold'
 
+  withLabel: trackStart {
+    executor = 'local'
+  }
   withName: getBag {
     executor = 'local'
   }

workflow/nextflow.config

@@ -11,9 +11,6 @@ profiles {
 }
 
 process {
-  withName:trackStart {
-    container = 'bicf/awscli:1.1'
-  }
   withName:getBag {
     container = 'bicf/gudmaprbkfilexfer:1.3'
   }

workflow/rna-seq.nf

@@ -47,6 +47,7 @@ script_inferMeta = Channel.fromPath("${baseDir}/scripts/inferMeta.sh")
 /*
  * trackStart: track start of pipeline
  */
+params.ci = false
 process trackStart {
   script:
   """
@@ -54,15 +55,15 @@ process trackStart {
   ulimit -a
   export https_proxy=\${http_proxy}
   
-  aws dynamodb put-item \
-    --table-name pipeline.tracking \
-    --item '{ \
-      "sessionId": {"S": "${workflow.sessionId}"}, \
-      "pipeline": {"S": "GUDMAP/RBK RNA-Seq"}, \
-      "start": {"S": "${workflow.start}"}, \
-      "astrocyte": {"BOOL": false}, \
-      "status": {"S": "started"}, \
-      "nextflowVersion": {"S": "${workflow.nextflow.version}"}}'
+  curl -H 'Content-Type: application/json' -X PUT -d '{ \
+      "sessionId": "${workflow.sessionId}", \
+      "pipeline": "gudmap.rbk_rnaseq", \
+      "start": "${workflow.start}", \
+      "astrocyte": false, \
+      "status": "started", \
+      "nextflowVersion": "${workflow.nextflow.version}",
+      "ci": ${params.ci}}' \
+  "https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
   """
  }