singularity support

Author: edsu7

process/score_upload.nf

@@ -34,6 +34,10 @@ process scoreUpload {
 
     container "${ params.score_container ?: params.container}:${params.score_container_version ?: params.container_version}"
 
+    if (workflow.containerEngine == "singularity") {
+        containerOptions "--bind ${workDir}:/song-client/logs"
+    }
+
     tag "${analysis_id}"
 
     input:

process/song_manifest.nf

@@ -37,6 +37,10 @@ process songManifest {
     memory "${params.mem} GB"
     tag "${analysis_id}"
 
+    if (workflow.containerEngine == "singularity") {
+        containerOptions "--bind ${workDir}:/song-client/logs"
+    }
+
     input:
         val study_id
         val analysis_id

process/song_publish.nf

@@ -33,6 +33,10 @@ process songPublish {
 
     container "${ params.song_container ?: params.container}:${params.song_container_version ?: params.container_version}"
 
+    if (workflow.containerEngine == "singularity") {
+        containerOptions "--bind ${workDir}:/song-client/logs"
+    }
+
     tag "${analysis_id}"
 
     input:

process/song_submit.nf

@@ -33,6 +33,10 @@ process songSubmit {
 
     container "${ params.song_container ?: params.container}:${params.song_container_version ?: params.container_version}"
 
+    if (workflow.containerEngine == "singularity") {
+        containerOptions "--bind ${workDir}:/song-client/logs"
+    }
+        
     tag "${study_id}"
     label "songSubmit"
 

song-score-upload/tests/checker.nf

@@ -43,16 +43,28 @@ params.song_cpus = 1
 params.song_mem = 1  // GB
 params.song_url = "https://song.rdpc-qa.cancercollaboratory.org"
 params.song_api_token = ""
-params.song_container_version = "4.2.1"
+params.song_container = "ghcr.io/overture-stack/song-client"
+params.song_container_version = "5.0.2"
 
 params.score_cpus = 1
 params.score_mem = 1  // GB
 params.score_transport_mem = 1  // GB
 params.score_url = "https://score.rdpc-qa.cancercollaboratory.org"
 params.score_api_token = ""
-params.score_container_version = "5.0.0"
-
-include { SongScoreUpload as SSUp } from '../main'
+params.score_container = "ghcr.io/overture-stack/score"
+params.score_container_version = "5.8.1"
+
+song_params = [
+    *:params,
+    'cpus': params.song_cpus,
+    'mem': params.song_mem,
+    'song_url': params.song_url,
+    'song_container': params.song_container,
+    'song_container_version': params.song_container_version,
+    'api_token': params.song_api_token ?: params.api_token
+]
+
+include { SongScoreUpload as SSUp } from '../main' params(song_params)
 
 
 workflow checker {