add docker mount log support

edsu7 · edsu7 · commit 5f29548a03e4 · 2023-01-05T13:57:12.000-05:00
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}"

Original file line number	Diff line number	Diff line change
`@@ -36,6 +36,8 @@ process scoreUpload {`
`36`	`36`
`37`	`37`	`if (workflow.containerEngine == "singularity") {`
`38`	`38`	`containerOptions "--bind \$(pwd):/score-client/logs"`
	`39`	`+ } else if (workflow.containerEngine == "docker") {`
	`40`	`+ containerOptions "-v \$(pwd):/score-client/logs"`
`39`	`41`	`}`
`40`	`42`
`41`	`43`	`tag "${analysis_id}"`
Original file line number	Diff line number	Diff line change
`@@ -39,6 +39,8 @@ process songManifest {`
`39`	`39`
`40`	`40`	`if (workflow.containerEngine == "singularity") {`
`41`	`41`	`containerOptions "--bind \$(pwd):/song-client/logs"`
	`42`	`+ } else if (workflow.containerEngine == "docker") {`
	`43`	`+ containerOptions "-v \$(pwd):/song-client/logs"`
`42`	`44`	`}`
`43`	`45`
`44`	`46`	`input:`
Original file line number	Diff line number	Diff line change
`@@ -35,6 +35,8 @@ process songPublish {`
`35`	`35`
`36`	`36`	`if (workflow.containerEngine == "singularity") {`
`37`	`37`	`containerOptions "--bind \$(pwd):/song-client/logs"`
	`38`	`+ } else if (workflow.containerEngine == "docker") {`
	`39`	`+ containerOptions "-v \$(pwd):/song-client/logs"`
`38`	`40`	`}`
`39`	`41`
`40`	`42`	`tag "${analysis_id}"`
Original file line number	Diff line number	Diff line change
`@@ -35,6 +35,8 @@ process songSubmit {`
`35`	`35`
`36`	`36`	`if (workflow.containerEngine == "singularity") {`
`37`	`37`	`containerOptions "--bind \$(pwd):/song-client/logs"`
	`38`	`+ } else if (workflow.containerEngine == "docker") {`
	`39`	`+ containerOptions "-v \$(pwd):/song-client/logs"`
`38`	`40`	`}`
`39`	`41`
`40`	`42`	`tag "${study_id}"`