add force flag

Author: edsu7

.DS_Store

@@ -15,7 +15,7 @@ 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}
         """
 }

process/score_upload.nf

@@ -51,6 +51,7 @@ 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 = "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)

song-score-upload/.DS_Store

@@ -53,6 +53,7 @@ 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 = "latest"
+params.score_force = false
 
 song_params = [
     *:params,