Merge pull request #50 from icgc-argo-workflows/song-score-download@2.9.0

[release]

Author: edsu7

process/score_download.nf

@@ -41,6 +41,12 @@ process scoreDownload {
     label "scoreDownload"
     tag "${analysis_id}"
 
+    if (workflow.containerEngine == "singularity") {
+        containerOptions "--bind \$(pwd):/score-client/logs"
+    } else if (workflow.containerEngine == "docker") {
+        containerOptions "-v \$(pwd):/score-client/logs"
+    }
+
     input:
         path analysis
         val study_id

process/song_get_analysis.nf

@@ -38,6 +38,12 @@ process songGetAnalysis {
 
     tag "${analysis_id}"
 
+    if (workflow.containerEngine == "singularity") {
+        containerOptions "--bind \$(pwd):/song-client/logs"
+    } else if (workflow.containerEngine == "docker") {
+        containerOptions "-v \$(pwd):/song-client/logs"
+    }
+
     input:
         val study_id
         val analysis_id

song-score-download/main.nf

@@ -21,7 +21,7 @@
 */
 
 nextflow.enable.dsl = 2
-version = '2.8.0'
+version = '2.9.0'
 
 // universal params go here, change default value as needed
 params.publish_dir = ""  // set to empty string will disable publishDir

song-score-download/pkg.json

@@ -1,6 +1,6 @@
 {
     "name": "song-score-download",
-    "version": "2.8.0",
+    "version": "2.9.0",
     "description": "SONG/SCORE download",
     "main": "main.nf",
     "deprecated": false,

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

@@ -1,5 +1,5 @@
 {
     "study_id": "TEST-PR",
-    "analysis_id": "9940db0f-c100-496a-80db-0fc100d96ac1",
+    "analysis_id": "b953d8e4-41d2-4334-93d8-e441d213346d",
     "publish_dir": "outdir"
 }

song-score-download/tests/local-test-2.json

@@ -1,6 +1,6 @@
 {
     "study_id": "TEST-PR",
-    "analysis_id": "9940db0f-c100-496a-80db-0fc100d96ac1",
+    "analysis_id": "b953d8e4-41d2-4334-93d8-e441d213346d",
     "max_retries": 3,
     "first_retry_wait_time": 5
 }

song-score-download/tests/local-test-3.json

@@ -1,5 +1,5 @@
 {
     "study_id": "TEST-PR",
-    "analysis_id": "9940db0f-c100-496a-80db-0fc100d96ac1",
+    "analysis_id": "b953d8e4-41d2-4334-93d8-e441d213346d",
     "max_retries": 0
 }