diff --git a/.DS_Store b/.DS_Store index 37d702a..44c83ff 100644 Binary files a/.DS_Store and b/.DS_Store differ diff --git a/process/score_upload.nf b/process/score_upload.nf index e2f644c..61ef9be 100644 --- 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 @@ -52,6 +52,7 @@ 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} @@ -59,6 +60,6 @@ process scoreUpload { 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 index 8854a21..43e45ad 100644 --- 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 index 91539a7..7d1f77e 100644 --- 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 index 4615b0a..4d322d6 100644 --- 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 new file mode 100644 index 0000000..8211dfa Binary files /dev/null and b/song-score-upload/.DS_Store differ diff --git a/song-score-upload/main.nf b/song-score-upload/main.nf index 978f5ff..87e6b55 100755 --- 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 @@ -42,7 +42,7 @@ 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 @@ -50,7 +50,8 @@ 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 index ab9f6b0..be5281e 100644 --- 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 index 2d30eec..7cf0ce1 100755 --- 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 @@ -44,7 +44,7 @@ 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 @@ -52,7 +52,8 @@ 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,