Merge pull request #53 from icgc-argo-workflows/[email protected]

[release]
icgc-argo-workflows · May 30, 2023 · 940d602 · 940d602
2 parents 530cb1e + 10ca12b
commit 940d602
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Showing 9 changed files with 18 additions and 14 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/process/score_upload.nf b/process/score_upload.nf
@@ -10,12 +10,12 @@ params.first_retry_wait_time = 1  // in seconds
 
 // required params w/ default
 params.container = "ghcr.io/overture-stack/score"
-params.container_version = "5.8.1"
+params.container_version = "latest"
 params.transport_mem = 2 // Transport memory is in number of GBs
 
 // optional if secret mounted from pod else required
 params.api_token = "" // song/score API token for download process
-
+params.score_force = false
 // required params, no default
 // --song_url         song url for download process
 // --score_url        score url for download process
@@ -52,13 +52,14 @@ process scoreUpload {
 
     script:
         accessToken = params.api_token ? params.api_token : "`cat /tmp/rdpc_secret/secret`"
+        forceFlag = params.score_force ? "--force" : ""
         """
         export METADATA_URL=${params.song_url}
         export STORAGE_URL=${params.score_url}
         export TRANSPORT_PARALLEL=${params.cpus}
         export TRANSPORT_MEMORY=${params.transport_mem}
         export ACCESSTOKEN=${accessToken}
         
-        score-client upload --manifest ${manifest}
+        score-client upload --manifest ${manifest} ${forceFlag}
         """
 }
diff --git a/process/song_manifest.nf b/process/song_manifest.nf
@@ -12,7 +12,7 @@ params.first_retry_wait_time = 1  // in seconds
 
 // required params w/ default
 params.container = "ghcr.io/overture-stack/song-client"
-params.container_version = "5.0.2"
+params.container_version = "latest"
 
 // optional if secret mounted from pod else required
 params.api_token = "" // song/score API token for download process

diff --git a/process/song_publish.nf b/process/song_publish.nf
@@ -10,7 +10,7 @@ params.first_retry_wait_time = 1  // in seconds
 
 // required params w/ default
 params.container = "ghcr.io/overture-stack/song-client"
-params.container_version = "5.0.2"
+params.container_version = "latest"
 
 // optional if secret mounted from pod else required
 params.api_token = "" // song/score API token for download process

diff --git a/process/song_submit.nf b/process/song_submit.nf
@@ -10,7 +10,7 @@ params.first_retry_wait_time = 1  // in seconds
 
 // required params w/ default
 params.container = "ghcr.io/overture-stack/song-client"
-params.container_version = "5.0.2"
+params.container_version = "latest"
 
 // optional if secret mounted from pod else required
 params.api_token = "" // song/score API token for download process

diff --git a/song-score-upload/.DS_Store b/song-score-upload/.DS_Store
diff --git a/song-score-upload/main.nf b/song-score-upload/main.nf
@@ -21,7 +21,7 @@
 */
 
 nextflow.enable.dsl = 2
-version = '2.9.2'
+version = '2.9.3'
 
 // universal params go here, change default value as needed
 params.publish_dir = ""  // set to empty string will disable publishDir
@@ -42,15 +42,16 @@ params.song_mem = 1  // GB
 params.song_url = "https://song.rdpc-qa.cancercollaboratory.org"
 params.song_api_token = ""
 params.song_container = "ghcr.io/overture-stack/song-client"
-params.song_container_version = "5.0.2"
+params.song_container_version = "latest"
 
 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 = "ghcr.io/overture-stack/score"
-params.score_container_version = "5.8.1"
+params.score_container_version = "latest"
+params.score_force = false
 
 song_params = [
     *:params,
@@ -71,7 +72,8 @@ score_params = [
     '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
+    'api_token': params.score_api_token ?: params.api_token,
+    'score_force': params.score_force
 ]
 
 include { songSubmit as songSub } from './local_modules/song-submit' params(song_params)

diff --git a/song-score-upload/pkg.json b/song-score-upload/pkg.json
@@ -1,6 +1,6 @@
 {
     "name": "song-score-upload",
-    "version": "2.9.2",
+    "version": "2.9.3",
     "description": "SONG/SCORE upload",
     "main": "main.nf",
     "deprecated": false,

diff --git a/song-score-upload/tests/checker.nf b/song-score-upload/tests/checker.nf
@@ -25,7 +25,7 @@
 */
 
 nextflow.enable.dsl = 2
-version = '2.9.2'
+version = '2.9.3'
 
 // universal params go here, change default value as needed
 params.max_retries = 5  // set to 0 will disable retry
@@ -44,15 +44,16 @@ params.song_mem = 1  // GB
 params.song_url = "https://song.rdpc-qa.cancercollaboratory.org"
 params.song_api_token = ""
 params.song_container = "ghcr.io/overture-stack/song-client"
-params.song_container_version = "5.0.2"
+params.song_container_version = "latest"
 
 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 = "ghcr.io/overture-stack/score"
-params.score_container_version = "5.8.1"
+params.score_container_version = "latest"
+params.score_force = false
 
 song_params = [
     *:params,