added publish_dir param

Author: junjun-zhang

process/song_manifest.nf

@@ -5,6 +5,8 @@ nextflow.enable.dsl=2
 params.cpus = 1
 params.mem = 1
 
+params.publish_dir = ""
+
 params.max_retries = 5  // set to 0 will disable retry
 params.first_retry_wait_time = 1  // in seconds
 
@@ -25,6 +27,8 @@ process songManifest {
         return params.max_retries ? 'retry' : 'finish'
     }
 
+    publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir
+
     pod = [secret: workflow.runName + "-secret", mountPath: "/tmp/rdpc_secret"]
 
     cpus params.cpus

song-score-upload/main.nf

@@ -24,6 +24,8 @@ nextflow.enable.dsl = 2
 version = '2.6.1'
 
 // universal params go here, change default value as needed
+params.publish_dir = ""  // set to empty string will disable publishDir
+
 params.max_retries = 5  // set to 0 will disable retry
 params.first_retry_wait_time = 1  // in seconds
 

song-score-upload/tests/local-test-1.json

@@ -1,5 +1,6 @@
 {
     "study_id": "TEST-PR",
     "payload": "data/9940db0f-c100-496a-80db-0fc100d96ac1.analysis.json",
-    "upload": ["data/SA610228.67.20200319.wxs.grch38.cram", "data/SA610228.67.20200319.wxs.grch38.cram.crai"]
+    "upload": ["data/SA610228.67.20200319.wxs.grch38.cram", "data/SA610228.67.20200319.wxs.grch38.cram.crai"],
+    "publish_dir": "outdir"
 }