Merge pull request #51 from icgc-argo-workflows/song-score-upload@2.9.2

[release]

Author: edsu7

process/score_upload.nf

@@ -36,6 +36,8 @@ process scoreUpload {
 
     if (workflow.containerEngine == "singularity") {
         containerOptions "--bind \$(pwd):/score-client/logs"
+    } else if (workflow.containerEngine == "docker") {
+        containerOptions "-v \$(pwd):/score-client/logs"
     }
 
     tag "${analysis_id}"

process/song_manifest.nf

@@ -39,6 +39,8 @@ process songManifest {
 
     if (workflow.containerEngine == "singularity") {
         containerOptions "--bind \$(pwd):/song-client/logs"
+    } else if (workflow.containerEngine == "docker") {
+        containerOptions "-v \$(pwd):/song-client/logs"
     }
 
     input:

process/song_publish.nf

@@ -35,6 +35,8 @@ process songPublish {
 
     if (workflow.containerEngine == "singularity") {
         containerOptions "--bind \$(pwd):/song-client/logs"
+    } else if (workflow.containerEngine == "docker") {
+        containerOptions "-v \$(pwd):/song-client/logs"
     }
 
     tag "${analysis_id}"

process/song_submit.nf

@@ -35,6 +35,8 @@ process songSubmit {
 
     if (workflow.containerEngine == "singularity") {
         containerOptions "--bind \$(pwd):/song-client/logs"
+    } else if (workflow.containerEngine == "docker") {
+        containerOptions "-v \$(pwd):/song-client/logs"
     }
 
     tag "${study_id}"

song-score-upload/main.nf

@@ -21,7 +21,7 @@
 */
 
 nextflow.enable.dsl = 2
-version = '2.9.1'
+version = '2.9.2'
 
 // universal params go here, change default value as needed
 params.publish_dir = ""  // set to empty string will disable publishDir

song-score-upload/pkg.json

@@ -1,6 +1,6 @@
 {
     "name": "song-score-upload",
-    "version": "2.9.1",
+    "version": "2.9.2",
     "description": "SONG/SCORE upload",
     "main": "main.nf",
     "deprecated": false,

song-score-upload/tests/checker.nf

@@ -25,7 +25,7 @@
 */
 
 nextflow.enable.dsl = 2
-version = '2.9.1'
+version = '2.9.2'
 
 // universal params go here, change default value as needed
 params.max_retries = 5  // set to 0 will disable retry