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Merge pull request #5 from icgc-argo-workflows/open-access-variant-fi…
…[email protected] [release]
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -23,15 +23,15 @@ | |
| nextflow.enable.dsl = 2 | ||
| name = 'open-access-variant-filtering' | ||
| short_name = 'open-filter' | ||
| version = '0.4.0' | ||
| version = '0.5.0' | ||
|
|
||
| // universal params go here, change default value as needed | ||
| params.container = "" | ||
| params.container_registry = "" | ||
| params.container_version = "" | ||
| params.cpus = 1 | ||
| params.mem = 1 // GB | ||
| params.publish_dir = "" // set to empty string will disable publishDir | ||
| params.cleanup = true | ||
| params.max_retries = 5 // set to 0 will disable retry | ||
| params.first_retry_wait_time = 1 // in seconds | ||
|
|
||
| // tool specific parmas go here, add / change as needed | ||
| params.study_id = "" | ||
|
|
@@ -59,33 +59,57 @@ params.open = true | |
| params.analysis_metadata = "NO_FILE_metadata" | ||
| params.vcf_file = "NO_FILE_vcf" | ||
|
|
||
| params.api_token = "" | ||
| // song/score setting | ||
| params.song_url = "" | ||
| params.song_container = "ghcr.io/overture-stack/song-client" | ||
| params.song_container_version = "5.0.2" | ||
| params.score_url = "" | ||
| params.cleanup = true | ||
| 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.upload = [:] | ||
| params.filter = [:] | ||
| params.payloadGenVcf = [:] | ||
|
|
||
| download_params = [ | ||
| '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_cpus': params.cpus, | ||
| 'score_mem': params.mem, | ||
| 'song_url': params.song_url, | ||
| 'score_url': params.score_url, | ||
| 'score_container': params.score_container, | ||
| '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, | ||
| 'publish_dir': params.publish_dir, | ||
| *:(params.download ?: [:]) | ||
| ] | ||
|
|
||
| upload_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_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, | ||
| 'publish_dir': params.publish_dir, | ||
| *:(params.upload ?: [:]) | ||
|
|
@@ -94,7 +118,7 @@ upload_params = [ | |
| filter_params = [ | ||
| 'cpus': params.cpus, | ||
| 'mem': params.mem, | ||
| 'publish_dir': '', | ||
| 'publish_dir': params.publish_dir, | ||
| 'regions_file': params.regions_file, | ||
| 'apply_filters': params.apply_filters, | ||
| 'output_type': params.output_type, | ||
|
|
@@ -110,11 +134,11 @@ payloadGenVcf_params = [ | |
| *:(params.payloadGenVcf ?: [:]) | ||
| ] | ||
|
|
||
| include { SongScoreDownload as dnVcf } from './wfpr_modules/github.com/icgc-argo/nextflow-data-processing-utility-tools/song-score-download@2.6.1/main.nf' params(download_params) | ||
| include { SongScoreDownload as dnVcf } 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 { metadataParser as mParser } from "./modules/raw.githubusercontent.com/icgc-argo/data-processing-utility-tools/metadata-parser.0.2.0.0/tools/metadata-parser/metadata-parser.nf" | ||
| include { variantFilter as vFilter } from './wfpr_modules/github.com/icgc-argo/variant-calling-tools/[email protected]/main.nf' params(filter_params) | ||
| include { payloadGenVariantProcessing as pGenVar } from "./wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/[email protected]/main.nf" params(payloadGenVcf_params) | ||
| include { SongScoreUpload as upVcf } from './wfpr_modules/github.com/icgc-argo/nextflow-data-processing-utility-tools/song-score-upload@2.6.1/main.nf' params(upload_params) | ||
| include { SongScoreUpload as upVcf } from './wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/main.nf' params(upload_params) | ||
| include { getSecondaryFiles as getSec } from './wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/[email protected]/main.nf' | ||
| include { cleanupWorkdir as cleanup } from './wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/[email protected]/main.nf' | ||
|
|
||
|
|
@@ -175,7 +199,7 @@ workflow OpenFilterWf { | |
| // skip upload if in local_mode | ||
| if (!local_mode) { | ||
| // uploadVariant | ||
| upVcf(study_id, pGenVar.out.payload, pGenVar.out.files_to_upload) | ||
| upVcf(study_id, pGenVar.out.payload, pGenVar.out.files_to_upload, '') | ||
| } | ||
|
|
||
| // cleanup, skip cleanup when running in local mode | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| { | ||
| "name": "open-access-variant-filtering-wf", | ||
| "version": "0.4.0", | ||
| "version": "0.5.0", | ||
| "description": "ICGC-ARGO Open-access Somatic Variant Filtering Workflow", | ||
| "main": "main.nf", | ||
| "deprecated": false, | ||
|
|
@@ -18,8 +18,8 @@ | |
| "github.com/icgc-argo/data-processing-utility-tools/[email protected]", | ||
| "github.com/icgc-argo-workflows/data-processing-utility-tools/[email protected]", | ||
| "github.com/icgc-argo/variant-calling-tools/[email protected]", | ||
| "github.com/icgc-argo/nextflow-data-processing-utility-tools/song-score-download@2.6.1", | ||
| "github.com/icgc-argo/nextflow-data-processing-utility-tools/song-score-upload@2.6.1" | ||
| "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" | ||
| ], | ||
| "devDependencies": [], | ||
| "contributors": [ | ||
|
|
||
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