Add trackStart process

workflow/conf/local.config

 process {
   executor = 'local'
 }
+
+singularity {
+  enabled = true
+  cacheDir = '/project/BICF/BICF_Core/shared/gudmap/singularity_cache/'
+}
+
+env {
+  http_proxy = 'http://proxy.swmed.edu:3128'
+  https_proxy = 'http://proxy.swmed.edu:3128'
+  all_proxy = 'http://proxy.swmed.edu:3128'
+}
\ No newline at end of file

workflow/main.nf

@@ -77,6 +77,23 @@ outDir = params.outDir
 multiqcConf = "${baseDir}/conf/multiqc_config.yaml"
 references = "${baseDir}/../docs/references.md"
 
+/*
+ * trackStart: track start of pipeline
+ */
+process trackStart {
+  script:
+  """
+  hostname
+  ulimit -a
+  export https_proxy=\${http_proxy}
+  
+  aws dynamodb put-item \
+    --table-name pipeline.tracking \
+      --item \
+        '{"sessionId": {"S": "${workflow.sessionId}"}, "pipeline": {"S": "cellranger_count"}, "projectDir": {"S": "${workflow.projectDir}"}, "start": {"S": "${workflow.start}"}, "astrocyte": {"BOOL": ${params.astrocyte}}}'
+  """
+  }
+
 /*
  * checkDesignFile: check design file for errors
  */

workflow/nextflow.config

@@ -14,6 +14,9 @@ profiles {
 }
 
 process {
+  withName:trackStart {
+    container = 'bicf/awscli:1.1'
+  }
   withName:checkDesignFile {
     container = 'bicf/python3:2.0.0'
   }