Merge pull request #39 from icgc-argo-workflows/song-score-upload@2.8.0

[release]

Author: lindaxiang

.github/workflows/build-test-release.yml

@@ -19,10 +19,13 @@ jobs:
     steps:
     - uses: actions/checkout@v2
 
-    - name: Set up Python 3.6
-      uses: actions/setup-python@v2
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
       with:
-        python-version: 3.6
+        python-version: "3.10"
+        architecture: "x64"
+      env:
+        AGENT_TOOLSDIRECTORY: /opt/hostedtoolcache
 
     - name: Extract package name and version from branch name
       id: get_pkg_info
@@ -80,10 +83,13 @@ jobs:
     steps:
     - uses: actions/checkout@v2
 
-    - name: Set up Python 3.6
-      uses: actions/setup-python@v2
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
       with:
-        python-version: 3.6
+        python-version: "3.10"
+        architecture: "x64"
+      env:
+        AGENT_TOOLSDIRECTORY: /opt/hostedtoolcache
 
     - name: Install dependencies
       run: |
@@ -177,6 +183,8 @@ jobs:
         body: |
           * Release `${{ steps.get_pkg_info.outputs.pkg_name }}.v${{ steps.get_pkg_info.outputs.pkg_ver }}` (${{ github.sha }})
           * Package `${{ steps.prep_assets.outputs.pkg_tar }}` (sha256: `${{ steps.prep_assets.outputs.pkg_tar_sha }}`)
+          * Package URI `github.com/${{ needs.build.outputs.repo_lowercase }}/${{ steps.get_pkg_info.outputs.pkg_name }}@${{ steps.get_pkg_info.outputs.pkg_ver }}`
+          * Run the package: `nextflow run ${{ needs.build.outputs.repo_lowercase }}/${{ steps.get_pkg_info.outputs.pkg_name }}/main.nf -r ${{ steps.get_pkg_info.outputs.pkg_name }}.v${{ steps.get_pkg_info.outputs.pkg_ver }} -params-file <params-json-file>`
         draft: false
         prerelease: false
 

process/score_download.nf

@@ -34,8 +34,8 @@ process scoreDownload {
     cpus params.cpus
     memory "${params.mem} GB"
 
-    container "overture/score:${params.container_version}"
-    publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir
+    container "overture/score:${params.score_container_version ?: params.container_version}"
+    publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir ? true : false
 
     label "scoreDownload"
     tag "${analysis_id}"

process/score_upload.nf

@@ -31,7 +31,7 @@ process scoreUpload {
     cpus params.cpus
     memory "${params.mem} GB"
 
-    container "overture/score:${params.container_version}"
+    container "overture/score:${params.score_container_version ?: params.container_version}"
 
     tag "${analysis_id}"
 

process/song_get_analysis.nf

@@ -32,8 +32,8 @@ process songGetAnalysis {
     cpus params.cpus
     memory "${params.mem} GB"
 
-    container "overture/song-client:${params.container_version}"
-    publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir
+    container "overture/song-client:${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

@@ -27,14 +27,14 @@ process songManifest {
         return params.max_retries ? 'retry' : 'finish'
     }
 
-    publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir
+    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:${params.container_version}"
+    container "overture/song-client:${params.song_container_version ?: params.container_version}"
 
     tag "${analysis_id}"
 

process/song_publish.nf

@@ -30,7 +30,7 @@ process songPublish {
     cpus params.cpus
     memory "${params.mem} GB"
 
-    container "overture/song-client:${params.container_version}"
+    container "overture/song-client:${params.song_container_version ?: params.container_version}"
 
     tag "${analysis_id}"
 

process/song_submit.nf

@@ -30,7 +30,7 @@ process songSubmit {
     cpus params.cpus
     memory "${params.mem} GB"
 
-    container "overture/song-client:${params.container_version}"
+    container "overture/song-client:${params.song_container_version ?: params.container_version}"
 
     tag "${study_id}"
     label "songSubmit"

song-score-upload/main.nf

@@ -21,7 +21,7 @@
 */
 
 nextflow.enable.dsl = 2
-version = '2.7.0'
+version = '2.8.0'
 
 // 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": "2.7.0",
+    "version": "2.8.0",
     "description": "SONG/SCORE upload",
     "main": "main.nf",
     "deprecated": false,

song-score-upload/tests/checker.nf

@@ -25,7 +25,7 @@
 */
 
 nextflow.enable.dsl = 2
-version = '0.2.6'  // package version
+version = '2.8.0'
 
 // universal params go here, change default value as needed
 params.max_retries = 5  // set to 0 will disable retry