change default to finish and other minor changes

Author: junjun-zhang

process/score_download.nf

@@ -26,7 +26,7 @@ process scoreDownload {
     maxRetries params.max_retries
     errorStrategy {
         sleep(Math.pow(2, task.attempt) * params.first_retry_wait_time * 1000 as long);  // backoff time increases exponentially before each retry
-        return params.max_retries ? 'retry' : 'terminate'
+        return params.max_retries ? 'retry' : 'finish'
     }
 
     pod = [secret: workflow.runName + "-secret", mountPath: "/tmp/rdpc_secret"]

process/song_get_analysis.nf

@@ -24,7 +24,7 @@ process songGetAnalysis {
     maxRetries params.max_retries
     errorStrategy {
         sleep(Math.pow(2, task.attempt) * params.first_retry_wait_time * 1000 as long);  // backoff time increases exponentially before each retry
-        return params.max_retries ? 'retry' : 'terminate'
+        return params.max_retries ? 'retry' : 'finish'
     }
 
     pod = [secret: workflow.runName + "-secret", mountPath: "/tmp/rdpc_secret"]

…download/local_modules/score_download.nf …download/local_modules/score-download.nfsong-score-download/local_modules/score_download.nf renamed to song-score-download/local_modules/score-download.nf song-score-download/local_modules/score_download.nf renamed to song-score-download/local_modules/score-download.nf

@@ -24,8 +24,6 @@ nextflow.enable.dsl = 2
 version = '2.6.0'  // package version
 
 // universal params go here, change default value as needed
-params.container = ""
-params.container_registry = ""
 params.publish_dir = ""  // set to empty string will disable publishDir
 
 params.max_retries = 5  // set to 0 will disable retry
@@ -73,8 +71,8 @@ score_params = [
 ]
 
 
-include { songGetAnalysis } from './local_modules/song_get_analysis' params(song_params)
-include { scoreDownload } from './local_modules/score_download' params(score_params)
+include { songGetAnalysis } from './local_modules/song-get-analysis' params(song_params)
+include { scoreDownload } from './local_modules/score-download' params(score_params)
 
 
 // please update workflow code as needed

…nload/local_modules/song_get_analysis.nf …nload/local_modules/song-get-analysis.nfsong-score-download/local_modules/song_get_analysis.nf renamed to song-score-download/local_modules/song-get-analysis.nf song-score-download/local_modules/song_get_analysis.nf renamed to song-score-download/local_modules/song-get-analysis.nf

@@ -50,24 +50,6 @@ params.score_transport_mem = 1  // GB
 params.score_url = "https://score.rdpc-qa.cancercollaboratory.org"
 params.score_api_token = ""
 
-song_params = [
-    *:params,
-    'cpus': params.song_cpus,
-    'mem': params.song_mem,
-    'song_url': params.song_url,
-    'api_token': params.song_api_token ?: params.api_token,
-    'publish_dir': ''
-]
-
-score_params = [
-    *:params,
-    'cpus': params.score_cpus,
-    'mem': params.score_mem,
-    'transport_mem': params.score_transport_mem,
-    'song_url': params.song_url,
-    'score_url': params.score_url,
-    'api_token': params.score_api_token ?: params.api_token
-]
 
 include { SongScoreDownload } from '../main'
 

song-score-download/main.nf

@@ -1,4 +1,6 @@
 {
     "study_id": "TEST-PR",
-    "analysis_id": "9940db0f-c100-496a-80db-0fc100d96ac1"
+    "analysis_id": "9940db0f-c100-496a-80db-0fc100d96ac1",
+    "max_retries": 3,
+    "first_retry_wait_time": 5
 }

song-score-download/tests/checker.nf

@@ -0,0 +1,5 @@
+{
+    "study_id": "TEST-PR",
+    "analysis_id": "9940db0f-c100-496a-80db-0fc100d96ac1",
+    "max_retries": 0
+}