update the release yaml file

icgc-argo-workflows · Apr 8, 2024 · dcbb851 · dcbb851
1 parent 4c5cb5d
commit dcbb851
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Showing 4 changed files with 21 additions and 14 deletions.
diff --git a/.github/workflows/build-test-release.yml b/.github/workflows/build-test-release.yml
@@ -19,10 +19,10 @@ jobs:
     steps:
     - uses: actions/checkout@v2
 
-    - name: Set up Python 3.11
+    - name: Set up Python 3.10
       uses: actions/setup-python@v3
       with:
-        python-version: 3.11
+        python-version: "3.10"
         architecture: "x64"
       env:
         AGENT_TOOLSDIRECTORY: /opt/hostedtoolcache
@@ -83,10 +83,10 @@ jobs:
     steps:
     - uses: actions/checkout@v2
 
-    - name: Set up Python 3.11
+    - name: Set up Python 3.10
       uses: actions/setup-python@v3
       with:
-        python-version: 3.11
+        python-version: "3.10"
         architecture: "x64"
       env:
         AGENT_TOOLSDIRECTORY: /opt/hostedtoolcache
@@ -183,6 +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
 
@@ -256,4 +258,4 @@ jobs:
         upload_url: ${{ steps.create_release.outputs.upload_url }}
         asset_path: ./pkg-release.json
         asset_name: pkg-release.json
-        asset_content_type: application/json
+        asset_content_type: application/json
diff --git a/example-params.local-qa.json b/example-params.local-qa.json
@@ -18,6 +18,8 @@
   "aln_qc": false,
   "song_url": "https://song.rdpc-qa.cumulus.genomeinformatics.org",
   "score_url": "https://score.rdpc-qa.cumulus.genomeinformatics.org",
+  "score_container_version": "5.10.0",
+  "song_container_version": "5.1.1",
   "download": {
     "score_mem": 4,
     "song_mem": 2,

diff --git a/example-params.rdpc-dev.json b/example-params.rdpc-dev.json
@@ -16,6 +16,8 @@
   "study_id":"TCRB-CA",
   "song_url": "https://song.rdpc-dev.cumulus.genomeinformatics.org",
   "score_url": "https://score.rdpc-dev.cumulus.genomeinformatics.org",
+  "score_container_version": "5.10.0",
+  "song_container_version": "5.1.1",
   "download":{
      "score_mem":10,
      "song_mem":2,
@@ -50,8 +52,8 @@
   "analysis_id":"580bd3ab-ddfb-46e5-8bd3-abddfb86e50a",
   "sjdboverhang":75,
   "starAligner":{
-     "mem":80,
-     "cpus":12
+     "mem":20,
+     "cpus":4
   },
   "ref_flat":"/nfs-dev-vol-qa-3/reference/rna-seq-references/GRCh38_Verily_v1.Picard_CollectRnaSeqMetrics/GRCh38_Verily_v1.refFlat.txt.gz",
   "cleanup":true,
@@ -60,8 +62,8 @@
 
   ],
   "hisat2Aligner":{
-     "mem":80,
-     "cpus":12
+     "mem":20,
+     "cpus":4
   },
   "bamMergeSortMarkdup":{
      "mem":18,

diff --git a/example-params.rdpc-qa.json b/example-params.rdpc-qa.json
@@ -12,12 +12,13 @@
   "ribosomal_interval_list": "/nfs-dev-vol-qa-3/reference/rna-seq-references/GRCh38_Verily_v1.Picard_CollectRnaSeqMetrics/GRCh38_Verily_v1.rRNA.interval_list",
   "cpus": 1,
   "mem": 4,
-  "tempdir": "/icgc-argo-scratch",
   "cleanup": true,
   "lane_qc": false,
   "aln_qc": false,
   "song_url": "https://song.rdpc-qa.cumulus.genomeinformatics.org",
   "score_url": "https://score.rdpc-qa.cumulus.genomeinformatics.org",
+  "score_container_version": "5.10.0",
+  "song_container_version": "5.1.1",
   "download": {
     "score_mem": 10,
     "song_mem": 2,
@@ -31,12 +32,12 @@
     "cpus": 4
   },
   "starAligner": {
-    "mem": 80,
-    "cpus": 12    
+    "mem": 30,
+    "cpus": 1    
   },
   "hisat2Aligner": {
-    "mem": 80,
-    "cpus": 12    
+    "mem": 20,
+    "cpus": 4    
   },
   "bamMergeSortMarkdup": {
     "mem": 18,