update song/score containers to ghcr

Author: lindaxiang

.wfpm

@@ -2,4 +2,4 @@ project_name: nextflow-data-processing-utility-tools
 license: Apache License 2.0
 repo_type: git
 repo_server: github.com
-repo_account: icgc-argo
+repo_account: icgc-argo-workflows

process/score_download.nf

@@ -11,7 +11,8 @@ params.max_retries = 5  // set to 0 will disable retry
 params.first_retry_wait_time = 1  // in seconds
 
 // required params w/ default
-params.container_version = "5.0.0"
+params.container = "ghcr.io/overture-stack/score"
+params.container_version = "5.8.1"
 params.transport_mem = 2 // Transport memory is in number of GBs
 
 // optional if secret mounted from pod else required
@@ -34,7 +35,7 @@ process scoreDownload {
     cpus params.cpus
     memory "${params.mem} GB"
 
-    container "overture/score:${params.score_container_version ?: params.container_version}"
+    container "${ params.score_container ?: params.container}:${params.score_container_version ?: params.container_version}"
     publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir ? true : false
 
     label "scoreDownload"

process/score_upload.nf

@@ -9,7 +9,8 @@ params.max_retries = 5  // set to 0 will disable retry
 params.first_retry_wait_time = 1  // in seconds
 
 // required params w/ default
-params.container_version = "5.0.0"
+params.container = "ghcr.io/overture-stack/score"
+params.container_version = "5.8.1"
 params.transport_mem = 2 // Transport memory is in number of GBs
 
 // optional if secret mounted from pod else required
@@ -30,8 +31,8 @@ process scoreUpload {
 
     cpus params.cpus
     memory "${params.mem} GB"
- 
-    container "overture/score:${params.score_container_version ?: params.container_version}"
+  
+    container "${ params.score_container ?: params.container}:${params.score_container_version ?: params.container_version}"
 
     tag "${analysis_id}"
 

process/song_get_analysis.nf

@@ -11,7 +11,8 @@ params.max_retries = 5  // set to 0 will disable retry
 params.first_retry_wait_time = 1  // in seconds
 
 // required params w/ default
-params.container_version = "4.2.1"
+params.container = "ghcr.io/overture-stack/song-client"
+params.container_version = "5.0.2"
 
 // optional if secret mounted from pod else required
 params.api_token = "" // song/score API token for download process
@@ -31,8 +32,8 @@ process songGetAnalysis {
 
     cpus params.cpus
     memory "${params.mem} GB"
- 
-    container "overture/song-client:${params.song_container_version ?: params.container_version}"
+    
+    container "${ params.song_container ?: params.container}:${params.song_container_version ?: params.container_version}"
     publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir ? true : false
 
     tag "${analysis_id}"

process/song_manifest.nf

@@ -11,7 +11,8 @@ params.max_retries = 5  // set to 0 will disable retry
 params.first_retry_wait_time = 1  // in seconds
 
 // required params w/ default
-params.container_version = "4.2.1"
+params.container = "ghcr.io/overture-stack/song-client"
+params.container_version = "5.0.2"
 
 // optional if secret mounted from pod else required
 params.api_token = "" // song/score API token for download process
@@ -27,15 +28,13 @@ process songManifest {
         return params.max_retries ? 'retry' : 'finish'
     }
 
+    container "${ params.song_container ?: params.container}:${params.song_container_version ?: params.container_version}"
     publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir ? true : false
 
     pod = [secret: workflow.runName + "-secret", mountPath: "/tmp/rdpc_secret"]
 
     cpus params.cpus
     memory "${params.mem} GB"
- 
-    container "overture/song-client:${params.song_container_version ?: params.container_version}"
-
     tag "${analysis_id}"
 
     input:

process/song_publish.nf

@@ -9,7 +9,8 @@ params.max_retries = 5  // set to 0 will disable retry
 params.first_retry_wait_time = 1  // in seconds
 
 // required params w/ default
-params.container_version = "4.2.1"
+params.container = "ghcr.io/overture-stack/song-client"
+params.container_version = "5.0.2"
 
 // optional if secret mounted from pod else required
 params.api_token = "" // song/score API token for download process
@@ -30,7 +31,7 @@ process songPublish {
     cpus params.cpus
     memory "${params.mem} GB"
 
-    container "overture/song-client:${params.song_container_version ?: params.container_version}"
+    container "${ params.song_container ?: params.container}:${params.song_container_version ?: params.container_version}"
 
     tag "${analysis_id}"
 

process/song_submit.nf

@@ -9,7 +9,8 @@ params.max_retries = 5  // set to 0 will disable retry
 params.first_retry_wait_time = 1  // in seconds
 
 // required params w/ default
-params.container_version = "4.2.1"
+params.container = "ghcr.io/overture-stack/song-client"
+params.container_version = "5.0.2"
 
 // optional if secret mounted from pod else required
 params.api_token = "" // song/score API token for download process
@@ -30,7 +31,7 @@ process songSubmit {
     cpus params.cpus
     memory "${params.mem} GB"
 
-    container "overture/song-client:${params.song_container_version ?: params.container_version}"
+    container "${ params.song_container ?: params.container}:${params.song_container_version ?: params.container_version}"
 
     tag "${study_id}"
     label "songSubmit"

song-score-download/main.nf

@@ -21,7 +21,7 @@
 */
 
 nextflow.enable.dsl = 2
-version = '2.6.2'
+version = '2.8.0'
 
 // universal params go here, change default value as needed
 params.publish_dir = ""  // set to empty string will disable publishDir
@@ -30,30 +30,33 @@ params.max_retries = 5  // set to 0 will disable retry
 params.first_retry_wait_time = 1  // in seconds
 
 // tool specific parmas go here, add / change as needed
-params.study_id = "TEST-PR"
-params.analysis_id = "9940db0f-c100-496a-80db-0fc100d96ac1"
+params.study_id = ""
+params.analysis_id = ""
 
 params.api_token = ""
 
 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"
+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
 ]
@@ -65,6 +68,7 @@ score_params = [
     'transport_mem': params.score_transport_mem,
     'song_url': params.song_url,
     'score_url': params.score_url,
+    'score_container': params.score_container,
     'score_container_version': params.score_container_version,
     'api_token': params.score_api_token ?: params.api_token
 ]

song-score-download/pkg.json

@@ -1,6 +1,6 @@
 {
     "name": "song-score-download",
-    "version": "2.6.2",
+    "version": "2.8.0",
     "description": "SONG/SCORE download",
     "main": "main.nf",
     "deprecated": false,
@@ -12,7 +12,7 @@
     ],
     "repository": {
         "type": "git",
-        "url": "https://github.com/icgc-argo/nextflow-data-processing-utility-tools.git"
+        "url": "https://github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools.git"
     },
     "dependencies": [],
     "devDependencies": [],
@@ -22,9 +22,12 @@
         },
         {
             "name": "Junjun Zhang"
+        },
+        {
+            "name": "Linda Xiang"
         }
     ],
     "license": "Apache License 2.0",
-    "bugReport": "https://github.com/icgc-argo/nextflow-data-processing-utility-tools/issues",
-    "homepage": "https://github.com/icgc-argo/nextflow-data-processing-utility-tools#readme"
+    "bugReport": "https://github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/issues",
+    "homepage": "https://github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools#readme"
 }

song-score-upload/main.nf

@@ -41,21 +41,23 @@ 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"
-
+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
 ]
@@ -67,6 +69,7 @@ score_params = [
     'transport_mem': params.score_transport_mem,
     'song_url': params.song_url,
     'score_url': params.score_url,
+    'score_container': params.score_container,
     'score_container_version': params.score_container_version,
     'api_token': params.score_api_token ?: params.api_token
 ]