diff --git a/dna-seq-alignment/main.nf b/dna-seq-alignment/main.nf index 1f85cb6..e157bef 100755 --- a/dna-seq-alignment/main.nf +++ b/dna-seq-alignment/main.nf @@ -1,7 +1,7 @@ #!/usr/bin/env nextflow nextflow.enable.dsl=2 name = 'dna-seq-alignment' -version = '1.9.1' +version = '1.9.2' /* ======================================================================================== @@ -126,13 +126,18 @@ params.file_info_tsv = "NO_FILE3" params.extra_info_tsv = "NO_FILE4" params.sequencing_files = [] +// song/score setting params.song_url = "" -params.song_container = "" -params.song_container_version = "" +params.song_container = "ghcr.io/overture-stack/song-client" +params.song_container_version = "5.0.2" params.score_url = "" -params.score_container = "" -params.score_container_version = "" +params.score_container = "ghcr.io/overture-stack/score" +params.score_container_version = "5.9.0" +params.score_mem = 20 +params.score_cpus = 8 +params.score_force = false params.api_token = "" + params.download = [:] params.seqDataToLaneBam = [:] params.bwaMemAligner = [:] @@ -147,16 +152,19 @@ params.gatkCollectOxogMetrics = [:] download_params = [ - 'cpus': params.cpus, - 'mem': params.mem, 'max_retries': params.max_retries, 'first_retry_wait_time': params.first_retry_wait_time, 'song_url': params.song_url, 'song_container': params.song_container, 'song_container_version': params.song_container_version, + 'song_cpus': params.cpus, + 'song_mem': params.mem, 'score_url': params.score_url, 'score_container': params.score_container, - 'score_container_version': params.score_container_version, + 'score_container_version': params.score_container_version, + 'score_cpus' : params.score_cpus, + 'score_mem' : params.score_mem, + 'score_transport_mem' : params.score_mem, 'api_token': params.api_token, *:(params.download ?: [:]) ] @@ -214,14 +222,18 @@ payloadGenDnaSeqQc_params = [ uploadAlignment_params = [ 'max_retries': params.max_retries, 'first_retry_wait_time': params.first_retry_wait_time, - 'cpus': params.cpus, - 'mem': params.mem, 'song_url': params.song_url, 'song_container': params.song_container, 'song_container_version': params.song_container_version, + 'song_cpus': params.cpus, + 'song_mem': params.mem, 'score_url': params.score_url, 'score_container': params.score_container, 'score_container_version': params.score_container_version, + 'score_force' : params.score_force, + 'score_cpus' : params.score_cpus, + 'score_mem' : params.score_mem, + 'score_transport_mem' : params.score_mem, 'api_token': params.api_token, *:(params.uploadAlignment ?: [:]) ] @@ -229,14 +241,18 @@ uploadAlignment_params = [ uploadQc_params = [ 'max_retries': params.max_retries, 'first_retry_wait_time': params.first_retry_wait_time, - 'cpus': params.cpus, - 'mem': params.mem, 'song_url': params.song_url, 'song_container': params.song_container, 'song_container_version': params.song_container_version, + 'song_cpus': params.cpus, + 'song_mem': params.mem, 'score_url': params.score_url, 'score_container': params.score_container, 'score_container_version': params.score_container_version, + 'score_force' : params.score_force, + 'score_cpus' : params.score_cpus, + 'score_mem' : params.score_mem, + 'score_transport_mem' : params.score_mem, 'api_token': params.api_token, *:(params.uploadQc ?: [:]) ] @@ -251,7 +267,7 @@ gatkCollectOxogMetrics_params = [ // Include all modules and pass params -include { SongScoreDownload as dnld } from './wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.8.0/main.nf' params(download_params) +include { SongScoreDownload as dnld } from './wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0/main.nf' params(download_params) include { seqDataToLaneBam as toLaneBam } from "./modules/raw.githubusercontent.com/icgc-argo/dna-seq-processing-tools/seq-data-to-lane-bam.0.3.3.0/tools/seq-data-to-lane-bam/seq-data-to-lane-bam.nf" params(seqDataToLaneBam_params) include { bwaMemAligner } from "./wfpr_modules/github.com/icgc-argo/dna-seq-processing-tools/bwa-mem-aligner@0.2.0/main.nf" params(bwaMemAligner_params) include { readGroupUBamQC as rgQC } from "./modules/raw.githubusercontent.com/icgc-argo/data-qc-tools-and-wfs/read-group-ubam-qc.0.1.2.0/tools/read-group-ubam-qc/read-group-ubam-qc.nf" params(readGroupUBamQC_params) @@ -263,8 +279,8 @@ include { payloadGenDnaSeqQc as pGenDnaSeqQc } from "./wfpr_modules/github.com/i include { gatkSplitIntervals as splitItvls; getSecondaryFiles as getSIIdx } from "./modules/raw.githubusercontent.com/icgc-argo/gatk-tools/gatk-split-intervals.4.1.4.1-1.0/tools/gatk-split-intervals/gatk-split-intervals" include { metadataParser as mParser } from "./modules/raw.githubusercontent.com/icgc-argo/data-processing-utility-tools/metadata-parser.0.1.0.0/tools/metadata-parser/metadata-parser.nf" include { gatkCollectOxogMetrics as oxog; getOxogSecondaryFiles; gatherOxogMetrics as gatherOM } from "./modules/raw.githubusercontent.com/icgc-argo/gatk-tools/gatk-collect-oxog-metrics.4.1.8.0-3.0/tools/gatk-collect-oxog-metrics/gatk-collect-oxog-metrics" params(gatkCollectOxogMetrics_params) -include { SongScoreUpload as upAln } from './wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/main.nf' params(uploadAlignment_params) -include { SongScoreUpload as upQc } from './wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/main.nf' params(uploadQc_params) +include { SongScoreUpload as upAln } from './wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/main.nf' params(uploadAlignment_params) +include { SongScoreUpload as upQc } from './wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/main.nf' params(uploadQc_params) include { cleanupWorkdir as cleanup } from './modules/raw.githubusercontent.com/icgc-argo/nextflow-data-processing-utility-tools/2.3.0/process/cleanup-workdir' include { payloadGenSeqExperiment as pGenExp } from './wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-seq-experiment@0.5.0/main.nf' diff --git a/dna-seq-alignment/pkg.json b/dna-seq-alignment/pkg.json index e5d1b13..1c813e2 100644 --- a/dna-seq-alignment/pkg.json +++ b/dna-seq-alignment/pkg.json @@ -1,6 +1,6 @@ { "name": "dna-seq-alignment", - "version": "1.9.1", + "version": "1.9.2", "description": "ICGC ARGO DNA Seq Processing Workflow", "main": "main.nf", "deprecated": false, @@ -14,14 +14,14 @@ "url": "https://github.com/icgc-argo-workflows/dna-seq-processing-wfs.git" }, "dependencies": [ - "github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.8.0", - "github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0", - "github.com/icgc-argo/dna-seq-processing-tools/bwa-mem-aligner@0.2.0", - "github.com/icgc-argo/dna-seq-processing-tools/bam-merge-sort-markdup@0.2.0", - "github.com/icgc-argo/data-processing-utility-tools/payload-gen-seq-experiment@0.5.0", - "github.com/icgc-argo/data-processing-utility-tools/payload-gen-dna-alignment@0.4.0", - "github.com/icgc-argo/data-processing-utility-tools/payload-gen-dna-seq-qc@0.6.0", - "github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1" + "github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0", + "github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3", + "github.com/icgc-argo/dna-seq-processing-tools/bwa-mem-aligner@0.2.0", + "github.com/icgc-argo/dna-seq-processing-tools/bam-merge-sort-markdup@0.2.0", + "github.com/icgc-argo/data-processing-utility-tools/payload-gen-seq-experiment@0.5.0", + "github.com/icgc-argo/data-processing-utility-tools/payload-gen-dna-alignment@0.4.0", + "github.com/icgc-argo/data-processing-utility-tools/payload-gen-dna-seq-qc@0.6.0", + "github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1" ], "devDependencies": [], "contributors": [ diff --git a/dna-seq-alignment/tests/local-test-bam.json b/dna-seq-alignment/tests/local-test-bam.json index d25dd14..21ff2fb 100644 --- a/dna-seq-alignment/tests/local-test-bam.json +++ b/dna-seq-alignment/tests/local-test-bam.json @@ -13,7 +13,9 @@ "song_mem": 2, "score_url": "https://submission-score.rdpc-qa.cancercollaboratory.org", "score_cpus": 3, - "score_mem": 8 + "score_mem": 8, + "score_transport_mem" : 8, + "score_container_version": "latest" }, "seqDataToLaneBam": { "cpus": 2, @@ -51,12 +53,15 @@ "song_cpus": 2, "song_mem": 2, "score_cpus": 3, - "score_mem": 8 + "score_mem": 8, + "score_transport_mem" : 8, + "score_force": true }, "uploadQc": { "song_cpus": 1, "song_mem": 1, "score_cpus": 1, - "score_mem": 1 + "score_mem": 4, + "score_transport_mem" : 4 } } diff --git a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.8.0/local_modules/score-download.nf b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0/local_modules/score-download.nf similarity index 90% rename from wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.8.0/local_modules/score-download.nf rename to wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0/local_modules/score-download.nf index a2e86cd..5829acf 100644 --- a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.8.0/local_modules/score-download.nf +++ b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0/local_modules/score-download.nf @@ -41,6 +41,12 @@ process scoreDownload { label "scoreDownload" tag "${analysis_id}" + if (workflow.containerEngine == "singularity") { + containerOptions "--bind \$(pwd):/score-client/logs" + } else if (workflow.containerEngine == "docker") { + containerOptions "-v \$(pwd):/score-client/logs" + } + input: path analysis val study_id diff --git a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.8.0/local_modules/song-get-analysis.nf b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0/local_modules/song-get-analysis.nf similarity index 88% rename from wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.8.0/local_modules/song-get-analysis.nf rename to wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0/local_modules/song-get-analysis.nf index 2cfb8ae..596dbe9 100644 --- a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.8.0/local_modules/song-get-analysis.nf +++ b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0/local_modules/song-get-analysis.nf @@ -38,6 +38,12 @@ process songGetAnalysis { tag "${analysis_id}" + if (workflow.containerEngine == "singularity") { + containerOptions "--bind \$(pwd):/song-client/logs" + } else if (workflow.containerEngine == "docker") { + containerOptions "-v \$(pwd):/song-client/logs" + } + input: val study_id val analysis_id diff --git a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.8.0/main.nf b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0/main.nf similarity index 99% rename from wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.8.0/main.nf rename to wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0/main.nf index ae70fc1..d07709b 100755 --- a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.8.0/main.nf +++ b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0/main.nf @@ -21,7 +21,7 @@ */ nextflow.enable.dsl = 2 -version = '2.8.0' +version = '2.9.0' // universal params go here, change default value as needed params.publish_dir = "" // set to empty string will disable publishDir diff --git a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.8.0/nextflow.config b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0/nextflow.config similarity index 100% rename from wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.8.0/nextflow.config rename to wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0/nextflow.config diff --git a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.8.0/pkg.json b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0/pkg.json similarity index 97% rename from wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.8.0/pkg.json rename to wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0/pkg.json index 9122ea7..35bb9f3 100644 --- a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.8.0/pkg.json +++ b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0/pkg.json @@ -1,6 +1,6 @@ { "name": "song-score-download", - "version": "2.8.0", + "version": "2.9.0", "description": "SONG/SCORE download", "main": "main.nf", "deprecated": false, diff --git a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.8.0/wfpr_modules b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0/wfpr_modules similarity index 100% rename from wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.8.0/wfpr_modules rename to wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0/wfpr_modules diff --git a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/local_modules/score-upload.nf b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/local_modules/score-upload.nf similarity index 80% rename from wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/local_modules/score-upload.nf rename to wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/local_modules/score-upload.nf index 8874c18..61ef9be 100644 --- a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/local_modules/score-upload.nf +++ b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/local_modules/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 @@ -34,6 +34,12 @@ process scoreUpload { container "${ params.score_container ?: params.container}:${params.score_container_version ?: params.container_version}" + if (workflow.containerEngine == "singularity") { + containerOptions "--bind \$(pwd):/score-client/logs" + } else if (workflow.containerEngine == "docker") { + containerOptions "-v \$(pwd):/score-client/logs" + } + tag "${analysis_id}" input: @@ -46,6 +52,7 @@ process scoreUpload { script: accessToken = params.api_token ? params.api_token : "`cat /tmp/rdpc_secret/secret`" + forceFlag = params.score_force ? "--force" : "" """ export METADATA_URL=${params.song_url} export STORAGE_URL=${params.score_url} @@ -53,6 +60,6 @@ process scoreUpload { export TRANSPORT_MEMORY=${params.transport_mem} export ACCESSTOKEN=${accessToken} - score-client upload --manifest ${manifest} + score-client upload --manifest ${manifest} ${forceFlag} """ } diff --git a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/local_modules/song-manifest.nf b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/local_modules/song-manifest.nf similarity index 86% rename from wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/local_modules/song-manifest.nf rename to wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/local_modules/song-manifest.nf index 03bb921..43e45ad 100644 --- a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/local_modules/song-manifest.nf +++ b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/local_modules/song-manifest.nf @@ -12,7 +12,7 @@ params.first_retry_wait_time = 1 // in seconds // required params w/ default params.container = "ghcr.io/overture-stack/song-client" -params.container_version = "5.0.2" +params.container_version = "latest" // optional if secret mounted from pod else required params.api_token = "" // song/score API token for download process @@ -37,6 +37,12 @@ process songManifest { memory "${params.mem} GB" tag "${analysis_id}" + if (workflow.containerEngine == "singularity") { + containerOptions "--bind \$(pwd):/song-client/logs" + } else if (workflow.containerEngine == "docker") { + containerOptions "-v \$(pwd):/song-client/logs" + } + input: val study_id val analysis_id diff --git a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/local_modules/song-publish.nf b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/local_modules/song-publish.nf similarity index 85% rename from wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/local_modules/song-publish.nf rename to wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/local_modules/song-publish.nf index a3f71a1..7d1f77e 100644 --- a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/local_modules/song-publish.nf +++ b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/local_modules/song-publish.nf @@ -10,7 +10,7 @@ params.first_retry_wait_time = 1 // in seconds // required params w/ default params.container = "ghcr.io/overture-stack/song-client" -params.container_version = "5.0.2" +params.container_version = "latest" // optional if secret mounted from pod else required params.api_token = "" // song/score API token for download process @@ -33,6 +33,12 @@ process songPublish { container "${ params.song_container ?: params.container}:${params.song_container_version ?: params.container_version}" + if (workflow.containerEngine == "singularity") { + containerOptions "--bind \$(pwd):/song-client/logs" + } else if (workflow.containerEngine == "docker") { + containerOptions "-v \$(pwd):/song-client/logs" + } + tag "${analysis_id}" input: diff --git a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/local_modules/song-submit.nf b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/local_modules/song-submit.nf similarity index 85% rename from wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/local_modules/song-submit.nf rename to wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/local_modules/song-submit.nf index cabd954..4d322d6 100644 --- a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/local_modules/song-submit.nf +++ b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/local_modules/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 @@ -33,6 +33,12 @@ process songSubmit { container "${ params.song_container ?: params.container}:${params.song_container_version ?: params.container_version}" + if (workflow.containerEngine == "singularity") { + containerOptions "--bind \$(pwd):/song-client/logs" + } else if (workflow.containerEngine == "docker") { + containerOptions "-v \$(pwd):/song-client/logs" + } + tag "${study_id}" label "songSubmit" diff --git a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/main.nf b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/main.nf similarity index 94% rename from wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/main.nf rename to wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/main.nf index db96b36..87e6b55 100755 --- a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/main.nf +++ b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/main.nf @@ -21,7 +21,7 @@ */ nextflow.enable.dsl = 2 -version = '2.9.0' +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/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/nextflow.config b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/nextflow.config similarity index 100% rename from wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/nextflow.config rename to wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/nextflow.config diff --git a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/pkg.json b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/pkg.json similarity index 97% rename from wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/pkg.json rename to wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/pkg.json index 2e6d699..be5281e 100644 --- a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/pkg.json +++ b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/pkg.json @@ -1,6 +1,6 @@ { "name": "song-score-upload", - "version": "2.9.0", + "version": "2.9.3", "description": "SONG/SCORE upload", "main": "main.nf", "deprecated": false, diff --git a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/wfpr_modules b/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/wfpr_modules similarity index 100% rename from wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.0/wfpr_modules rename to wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/wfpr_modules