Merge pull request #51 from icgc-argo-workflows/[email protected]

[release]
icgc-argo-workflows · Jan 6, 2023 · 5d79bcb · 5d79bcb
2 parents 2ebb385 + 5f29548
commit 5d79bcb
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Showing 7 changed files with 11 additions and 3 deletions.
diff --git a/process/score_upload.nf b/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}"

diff --git a/process/song_manifest.nf b/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:

diff --git a/process/song_publish.nf b/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}"

diff --git a/process/song_submit.nf b/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}"

diff --git a/song-score-upload/main.nf b/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

diff --git a/song-score-upload/pkg.json b/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,

diff --git a/song-score-upload/tests/checker.nf b/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