From 921b6bf03ca3f7d5c48fd20f2d6bc96e5db5d866 Mon Sep 17 00:00:00 2001 From: edsu7 <22638361+edsu7@users.noreply.github.com> Date: Tue, 30 May 2023 11:44:13 -0400 Subject: [PATCH 1/7] [wfpm v0.8.0] started a new version argo-data-submission-wf@1.0.2 from argo-data-submission-wf@1.0.1 which was released --- argo-data-submission-wf/main.nf | 2 +- argo-data-submission-wf/pkg.json | 2 +- argo-data-submission-wf/tests/checker.nf | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/argo-data-submission-wf/main.nf b/argo-data-submission-wf/main.nf index 51adebe..90818f6 100755 --- a/argo-data-submission-wf/main.nf +++ b/argo-data-submission-wf/main.nf @@ -22,7 +22,7 @@ */ nextflow.enable.dsl = 2 -version = '1.0.1' +version = '1.0.2' // universal params go here, change default value as needed params.container = "" diff --git a/argo-data-submission-wf/pkg.json b/argo-data-submission-wf/pkg.json index a271884..86bdac2 100644 --- a/argo-data-submission-wf/pkg.json +++ b/argo-data-submission-wf/pkg.json @@ -1,6 +1,6 @@ { "name": "argo-data-submission-wf", - "version": "1.0.1", + "version": "1.0.2", "description": "ARGO data submission workflow", "main": "main.nf", "deprecated": false, diff --git a/argo-data-submission-wf/tests/checker.nf b/argo-data-submission-wf/tests/checker.nf index ef6c4d6..5324c9a 100755 --- a/argo-data-submission-wf/tests/checker.nf +++ b/argo-data-submission-wf/tests/checker.nf @@ -26,7 +26,7 @@ */ nextflow.enable.dsl = 2 -version = '1.0.1' +version = '1.0.2' // universal params params.publish_dir = "" From 906171f5db9b06a2efafa3798ed85192247d5cbe Mon Sep 17 00:00:00 2001 From: edsu7 <22638361+edsu7@users.noreply.github.com> Date: Tue, 30 May 2023 12:58:18 -0400 Subject: [PATCH 2/7] bump score version and add score flags --- argo-data-submission-wf/main.nf | 14 ++++++++++++-- argo-data-submission-wf/pkg.json | 4 ++-- nextflow.config | 2 +- .../local_modules/score-upload.nf | 7 ++++--- .../local_modules/song-manifest.nf | 2 +- .../local_modules/song-publish.nf | 2 +- .../local_modules/song-submit.nf | 2 +- .../main.nf | 10 ++++++---- .../nextflow.config | 0 .../pkg.json | 2 +- .../wfpr_modules | 0 11 files changed, 29 insertions(+), 16 deletions(-) rename wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/{song-score-upload@2.9.2 => song-score-upload@2.9.3}/local_modules/score-upload.nf (91%) rename wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/{song-score-upload@2.9.2 => song-score-upload@2.9.3}/local_modules/song-manifest.nf (98%) rename wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/{song-score-upload@2.9.2 => song-score-upload@2.9.3}/local_modules/song-publish.nf (98%) rename wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/{song-score-upload@2.9.2 => song-score-upload@2.9.3}/local_modules/song-submit.nf (98%) rename wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/{song-score-upload@2.9.2 => song-score-upload@2.9.3}/main.nf (94%) rename wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/{song-score-upload@2.9.2 => song-score-upload@2.9.3}/nextflow.config (100%) rename wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/{song-score-upload@2.9.2 => song-score-upload@2.9.3}/pkg.json (97%) rename wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/{song-score-upload@2.9.2 => song-score-upload@2.9.3}/wfpr_modules (100%) diff --git a/argo-data-submission-wf/main.nf b/argo-data-submission-wf/main.nf index 90818f6..4ed3831 100755 --- a/argo-data-submission-wf/main.nf +++ b/argo-data-submission-wf/main.nf @@ -30,6 +30,7 @@ params.container_registry = "" params.container_version = "" params.cpus = 1 params.mem = 1 // GB +params.force = false params.publish_dir = "" // set to empty string will disable publishDir // tool specific parmas go here, add / change as needed @@ -44,6 +45,9 @@ params.song_container = "" params.song_container_version = "" params.score_container = "" params.score_container_version = "" +params.score_mem = 2 +params.score_cpus = 4 +params.score_force = false // sanityChecks params.song_url="" @@ -131,6 +135,12 @@ upload_params = [ 'first_retry_wait_time': params.first_retry_wait_time, 'cpus': params.cpus, 'mem': params.mem, + 'score_force' : params.score_force, + 'score_cpus' : params.score_cpus, + 'score_mem' : params.score_mem, + 'score_transport_mem' : params.score_mem, + 'song_cpus' : params.cpus, + 'song_mem' : params.mem, 'song_url': params.song_url, 'song_container': params.song_container, 'song_container_version': params.song_container_version, @@ -156,7 +166,7 @@ submissionReceipt_params = [ 'mem': params.mem, ] -include { SongScoreUpload as uploadWf } from './wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.2/main.nf' params(upload_params) +include { SongScoreUpload as uploadWf } 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 { validateSeqtools as valSeq} from './wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/main.nf' params(validateSeq_params) include { EgaDownloadWf as egaWf } from './wfpr_modules/github.com/icgc-argo/argo-data-submission/ega-download-wf@0.1.6/main.nf' params(egaDownload_params) include { payloadGenSeqExperiment as pGenExp} from './wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/main.nf' params(payloadGen_params) @@ -461,4 +471,4 @@ workflow { params.song_url, params.clinical_url ) -} \ No newline at end of file +} diff --git a/argo-data-submission-wf/pkg.json b/argo-data-submission-wf/pkg.json index 86bdac2..7ee242d 100644 --- a/argo-data-submission-wf/pkg.json +++ b/argo-data-submission-wf/pkg.json @@ -20,7 +20,7 @@ "github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1", "github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1", "github.com/icgc-argo/argo-data-submission/submission-receipt@0.1.0", - "github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.2" + "github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3" ], "devDependencies": [], "contributors": [ @@ -36,4 +36,4 @@ "license": "GNU Affero General Public License v3", "bugReport": "https://github.com/icgc-argo/argo-data-submission/issues", "homepage": "https://github.com/icgc-argo/argo-data-submission#readme" -} \ No newline at end of file +} diff --git a/nextflow.config b/nextflow.config index 14ab950..b39f351 100644 --- a/nextflow.config +++ b/nextflow.config @@ -89,4 +89,4 @@ profiles { params.clinical_url = 'https://clinical.dev.argo.cancercollaboratory.org' params.schema_url = 'https://submission-song.rdpc-dev.cancercollaboratory.org/schemas/sequencing_experiment' } -} \ No newline at end of file +} diff --git a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.2/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 91% rename from wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.2/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 e2f644c..61ef9be 100644 --- a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.2/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 @@ -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/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.2/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 98% rename from wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.2/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 8854a21..43e45ad 100644 --- a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.2/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 diff --git a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.2/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 98% rename from wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.2/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 91539a7..7d1f77e 100644 --- a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.2/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 diff --git a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.2/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 98% rename from wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.2/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 4615b0a..4d322d6 100644 --- a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.2/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 diff --git a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.2/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@2.9.2/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 978f5ff..87e6b55 100755 --- a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.2/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 = '2.9.2' +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/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.2/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@2.9.2/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@2.9.2/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@2.9.2/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 ab9f6b0..be5281e 100644 --- a/wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.2/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": "2.9.2", + "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@2.9.2/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@2.9.2/wfpr_modules rename to wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/wfpr_modules From 3ab636211baa4b5f183145a6e373f80772b49414 Mon Sep 17 00:00:00 2001 From: edsu7 <22638361+edsu7@users.noreply.github.com> Date: Fri, 9 Jun 2023 13:29:59 -0400 Subject: [PATCH 3/7] added updates for `payload-json-to-tsvs' and `payload-gen-seq-exp` --- argo-data-submission-wf/main.nf | 6 +-- argo-data-submission-wf/pkg.json | 4 +- argo-data-submission-wf/tests/file.v2.tsv | 7 ---- .../experiment-fq.badWXS.tsv} | 2 +- .../tests/input/experiment-fq.goodWXS.tsv | 2 + ...-test-job-14-problem-missingWXSfields.json | 8 ++++ .../tests/local-test-job-15-WXS.json | 8 ++++ .../tests/read_group.v2.tsv | 4 -- .../.dockerignore | 0 .../.gitignore | 0 .../Dockerfile | 0 .../main.nf | 2 +- .../main.py | 38 ++++++++++++++----- .../nextflow.config | 0 .../pkg.json | 2 +- .../wfpr_modules | 0 .../.dockerignore | 0 .../Dockerfile | 0 .../README.md | 0 .../main.nf | 2 +- .../main.py | 6 +-- .../nextflow.config | 0 .../pkg.json | 2 +- .../wfpr_modules | 0 24 files changed, 58 insertions(+), 35 deletions(-) delete mode 100644 argo-data-submission-wf/tests/file.v2.tsv rename argo-data-submission-wf/tests/{experiment.v2.tsv => input/experiment-fq.badWXS.tsv} (55%) create mode 100644 argo-data-submission-wf/tests/input/experiment-fq.goodWXS.tsv create mode 100644 argo-data-submission-wf/tests/local-test-job-14-problem-missingWXSfields.json create mode 100644 argo-data-submission-wf/tests/local-test-job-15-WXS.json delete mode 100644 argo-data-submission-wf/tests/read_group.v2.tsv rename wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/{payload-gen-seq-experiment@0.8.2 => payload-gen-seq-experiment@0.8.3}/.dockerignore (100%) rename wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/{payload-gen-seq-experiment@0.8.2 => payload-gen-seq-experiment@0.8.3}/.gitignore (100%) rename wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/{payload-gen-seq-experiment@0.8.2 => payload-gen-seq-experiment@0.8.3}/Dockerfile (100%) rename wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/{payload-gen-seq-experiment@0.8.2 => payload-gen-seq-experiment@0.8.3}/main.nf (99%) rename wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/{payload-gen-seq-experiment@0.8.2 => payload-gen-seq-experiment@0.8.3}/main.py (92%) rename wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/{payload-gen-seq-experiment@0.8.2 => payload-gen-seq-experiment@0.8.3}/nextflow.config (100%) rename wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/{payload-gen-seq-experiment@0.8.2 => payload-gen-seq-experiment@0.8.3}/pkg.json (97%) rename wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/{payload-gen-seq-experiment@0.8.2 => payload-gen-seq-experiment@0.8.3}/wfpr_modules (100%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{payload-json-to-tsvs@0.1.1 => payload-json-to-tsvs@0.1.2}/.dockerignore (100%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{payload-json-to-tsvs@0.1.1 => payload-json-to-tsvs@0.1.2}/Dockerfile (100%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{payload-json-to-tsvs@0.1.1 => payload-json-to-tsvs@0.1.2}/README.md (100%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{payload-json-to-tsvs@0.1.1 => payload-json-to-tsvs@0.1.2}/main.nf (99%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{payload-json-to-tsvs@0.1.1 => payload-json-to-tsvs@0.1.2}/main.py (96%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{payload-json-to-tsvs@0.1.1 => payload-json-to-tsvs@0.1.2}/nextflow.config (100%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{payload-json-to-tsvs@0.1.1 => payload-json-to-tsvs@0.1.2}/pkg.json (97%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{payload-json-to-tsvs@0.1.1 => payload-json-to-tsvs@0.1.2}/wfpr_modules (100%) diff --git a/argo-data-submission-wf/main.nf b/argo-data-submission-wf/main.nf index 4ed3831..101d3c6 100755 --- a/argo-data-submission-wf/main.nf +++ b/argo-data-submission-wf/main.nf @@ -169,12 +169,12 @@ submissionReceipt_params = [ include { SongScoreUpload as uploadWf } 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 { validateSeqtools as valSeq} from './wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/main.nf' params(validateSeq_params) include { EgaDownloadWf as egaWf } from './wfpr_modules/github.com/icgc-argo/argo-data-submission/ega-download-wf@0.1.6/main.nf' params(egaDownload_params) -include { payloadGenSeqExperiment as pGenExp} from './wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/main.nf' params(payloadGen_params) +include { payloadGenSeqExperiment as pGenExp} from './wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/main.nf' params(payloadGen_params) include { cleanupWorkdir as cleanup } from './wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/cleanup-workdir@1.0.0.1/main.nf' include { cram2bam } from './wfpr_modules/github.com/icgc-argo-workflows/dna-seq-processing-tools/cram2bam@0.1.0/main.nf' params(cram2bam_params) include { getSecondaryFiles } from './wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/helper-functions@1.0.1.1/main.nf' params([*:params, 'cleanup': false]) include { sanityCheck } from './wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/main.nf' params(sanityCheck_params) -include { payloadJsonToTsvs } from './wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1/main.nf' params(payloadJsonToTsvs_params) +include { payloadJsonToTsvs } from './wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/main.nf' params(payloadJsonToTsvs_params) include { submissionReceipt } from './wfpr_modules/github.com/icgc-argo/argo-data-submission/submission-receipt@0.1.0/main.nf' params(submissionReceipt_params) // please update workflow code as needed @@ -446,8 +446,6 @@ workflow ArgoDataSubmissionWf { uploadWf.out.analysis_id, submissionReceipt.out.receipt ) - //Channel.from(pGenExp.out.payload).view() - //Channel.of(pGenExp.out.payload).view() emit: json_file=pGenExp.out.payload diff --git a/argo-data-submission-wf/pkg.json b/argo-data-submission-wf/pkg.json index 7ee242d..79e75bf 100644 --- a/argo-data-submission-wf/pkg.json +++ b/argo-data-submission-wf/pkg.json @@ -14,10 +14,10 @@ "dependencies": [ "github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7", "github.com/icgc-argo/argo-data-submission/ega-download-wf@0.1.6", - "github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2", + "github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3", "github.com/icgc-argo-workflows/data-processing-utility-tools/cleanup-workdir@1.0.0.1", "github.com/icgc-argo-workflows/dna-seq-processing-tools/cram2bam@0.1.0", - "github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1", + "github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2", "github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1", "github.com/icgc-argo/argo-data-submission/submission-receipt@0.1.0", "github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3" diff --git a/argo-data-submission-wf/tests/file.v2.tsv b/argo-data-submission-wf/tests/file.v2.tsv deleted file mode 100644 index 87a8720..0000000 --- a/argo-data-submission-wf/tests/file.v2.tsv +++ /dev/null @@ -1,7 +0,0 @@ -type name format size md5sum path -file C0HVY.2_r1.fq.gz FASTQ 2040 c4971f805930e9e31e1c45314c652d3c input/C0HVY.2_r1.fq.gz -file C0HVY.2_r2.fq.gz FASTQ 2042 f60026e682bf55f014c84d494112aa13 input/C0HVY.2_r2.fq.gz -file D0RE2.1_r1.fq.gz FASTQ 2309 835b35f6e7f8263636fce4224b1aca69 input/D0RE2.1_r1.fq.gz -file D0RE2.1_r2.fq.gz FASTQ 2365 23d030ddba2916f8430b13234e3e9a0c input/D0RE2.1_r2.fq.gz -file D0RH0.2_r1.fq.gz FASTQ 1872 b3aa75d0585a989bb25fae252a10b532 input/D0RH0.2_r1.fq.gz -file D0RH0.2_r2.fq.gz FASTQ 1894 c59ebfa4199287bf3911a4c1d6eda71e input/D0RH0.2_r2.fq.gz \ No newline at end of file diff --git a/argo-data-submission-wf/tests/experiment.v2.tsv b/argo-data-submission-wf/tests/input/experiment-fq.badWXS.tsv similarity index 55% rename from argo-data-submission-wf/tests/experiment.v2.tsv rename to argo-data-submission-wf/tests/input/experiment-fq.badWXS.tsv index 45dadcb..781ba0b 100644 --- a/argo-data-submission-wf/tests/experiment.v2.tsv +++ b/argo-data-submission-wf/tests/input/experiment-fq.badWXS.tsv @@ -1,2 +1,2 @@ type submitter_sequencing_experiment_id program_id submitter_donor_id submitter_specimen_id submitter_sample_id submitter_matched_normal_sample_id sequencing_center platform platform_model experimental_strategy sequencing_date read_group_count -sequencing_experiment SubWf_exp_02_FASTQ_input TEST-QA TEST_SUBMITTER_DONOR_ID_aaupbblgaa TEST_SPECIMEN_DONOR_ID_aaupbblgaa TEST_SAMPLE_DONOR_ID_aaupbblgaa EXT ILLUMINA HiSeq 2000 WGS 2014-12-12 3 \ No newline at end of file +sequencing_experiment SubWf_exp_02_FASTQ_input TEST-QA SubWf_test_01 SubWf_test_01_SP_T SubWf_test_01_SA_T SubWf_test_01_SA_N EXT ILLUMINA HiSeq 2000 WXS 2014-12-12 3 \ No newline at end of file diff --git a/argo-data-submission-wf/tests/input/experiment-fq.goodWXS.tsv b/argo-data-submission-wf/tests/input/experiment-fq.goodWXS.tsv new file mode 100644 index 0000000..eaaaf38 --- /dev/null +++ b/argo-data-submission-wf/tests/input/experiment-fq.goodWXS.tsv @@ -0,0 +1,2 @@ +type submitter_sequencing_experiment_id program_id submitter_donor_id submitter_specimen_id submitter_sample_id submitter_matched_normal_sample_id sequencing_center platform platform_model experimental_strategy sequencing_date read_group_count target_capture_kit primary_target_regions capture_target_regions +sequencing_experiment SubWf_exp_02_FASTQ_input TEST-QA SubWf_test_01 SubWf_test_01_SP_T SubWf_test_01_SA_T SubWf_test_01_SA_N EXT ILLUMINA HiSeq 2000 WXS 2014-12-12 3 dummy_val dummy_val dummy_val diff --git a/argo-data-submission-wf/tests/local-test-job-14-problem-missingWXSfields.json b/argo-data-submission-wf/tests/local-test-job-14-problem-missingWXSfields.json new file mode 100644 index 0000000..48f52d6 --- /dev/null +++ b/argo-data-submission-wf/tests/local-test-job-14-problem-missingWXSfields.json @@ -0,0 +1,8 @@ +{ + "study_id": "TEST-QA", + "experiment_info_tsv": "input/experiment-fq.badWXS.tsv", + "read_group_info_tsv": "input/read_group-fq.v2.tsv", + "file_info_tsv": "input/file-fq.v2.tsv", + "download_mode": "local", + "publish_dir": "outdir" +} diff --git a/argo-data-submission-wf/tests/local-test-job-15-WXS.json b/argo-data-submission-wf/tests/local-test-job-15-WXS.json new file mode 100644 index 0000000..c55cc90 --- /dev/null +++ b/argo-data-submission-wf/tests/local-test-job-15-WXS.json @@ -0,0 +1,8 @@ +{ + "study_id": "TEST-QA", + "experiment_info_tsv": "input/experiment-fq.goodWXS.tsv", + "read_group_info_tsv": "input/read_group-fq.v2.tsv", + "file_info_tsv": "input/file-fq.v2.tsv", + "download_mode": "local", + "publish_dir": "outdir" +} diff --git a/argo-data-submission-wf/tests/read_group.v2.tsv b/argo-data-submission-wf/tests/read_group.v2.tsv deleted file mode 100644 index c31bff6..0000000 --- a/argo-data-submission-wf/tests/read_group.v2.tsv +++ /dev/null @@ -1,4 +0,0 @@ -type submitter_read_group_id read_group_id_in_bam submitter_sequencing_experiment_id platform_unit is_paired_end file_r1 file_r2 read_length_r1 read_length_r2 insert_size sample_barcode library_name -read_group C0HVY.2 SubWf_exp_02_FASTQ_input 74_8a true C0HVY.2_r1.fq.gz C0HVY.2_r2.fq.gz 150 150 298 Pond-147580 -read_group D0RE2.1 SubWf_exp_02_FASTQ_input 74_8b true D0RE2.1_r1.fq.gz D0RE2.1_r2.fq.gz 150 150 298 Pond-147580 -read_group D0RH0.2 SubWf_exp_02_FASTQ_input 74_8c true D0RH0.2_r1.fq.gz D0RH0.2_r2.fq.gz 150 150 298 Pond-147580 diff --git a/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/.dockerignore b/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/.dockerignore similarity index 100% rename from wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/.dockerignore rename to wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/.dockerignore diff --git a/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/.gitignore b/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/.gitignore similarity index 100% rename from wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/.gitignore rename to wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/.gitignore diff --git a/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/Dockerfile b/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/Dockerfile similarity index 100% rename from wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/Dockerfile rename to wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/Dockerfile diff --git a/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/main.nf b/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/main.nf similarity index 99% rename from wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/main.nf rename to wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/main.nf index 2b8c4cc..87e11f1 100755 --- a/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/main.nf +++ b/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/main.nf @@ -26,7 +26,7 @@ /* this block is auto-generated based on info from pkg.json where */ /* changes can be made if needed, do NOT modify this block manually */ nextflow.enable.dsl = 2 -version = '0.8.2' +version = '0.8.3' container = [ 'ghcr.io': 'ghcr.io/icgc-argo-workflows/data-processing-utility-tools.payload-gen-seq-experiment' diff --git a/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/main.py b/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/main.py similarity index 92% rename from wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/main.py rename to wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/main.py index 21f81bb..be08bbb 100755 --- a/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/main.py +++ b/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/main.py @@ -45,10 +45,12 @@ 'submitter_sample_id','sample_type', 'submitter_matched_normal_sample_id', 'sequencing_center', 'platform', 'platform_model','experimental_strategy', 'sequencing_date', 'read_group_count'] TSV_FIELDS['experiment']["conditional"]=[ - "library_isolation_protocol","library_preparation_kit", - "library_strandedness","rin","dv200","spike_ins_included", - "spike_ins_fasta","spike_ins_concentration", - "target_capture_kit"] + "library_preparation_kit", + "library_strandedness", + "rin","dv200", + "target_capture_kit","number_of_genes","gene_padding","coverage", + "primary_target_regions","capture_target_regions" + ] TSV_FIELDS['read_group']= {} TSV_FIELDS['read_group']["core"]=[ @@ -77,10 +79,10 @@ def empty_str_to_null(metadata): for k in metadata: - if k in ['read_groups', 'files']: + if k in ['read_groups', 'files','experiment']: for i in range(len(metadata[k])): empty_str_to_null(metadata[k][i]) - if isinstance(metadata[k], str) and metadata[k] in ["", "_NULL_"]: + if isinstance(metadata[k], str) and metadata[k] in ["", "_NULL_","null","NULL","Null","None","NONE","none"]: metadata[k] = None @@ -146,10 +148,20 @@ def load_all_tsvs(exp_tsv, rg_tsv, file_tsv): rg['is_paired_end'] = None for field in ('read_length_r1', 'read_length_r2', 'insert_size'): - if rg[field]: + if isinstance(rg[field],str): + if re.match("^[0-9]+$", rg[field]): + rg[field] = int(rg[field]) + continue + for empty_string in ["", "_NULL_",'null',"NULL","Null","None","NONE","none"]: + if rg[field]==empty_string: + rg[field] = None + break + elif isinstance(rg[field],int): rg[field] = int(rg[field]) - else: + elif rg[field] is None: rg[field] = None + else: + sys.exit("Unrecognnized value '%s' in field %s for '%s'" % (str(rg[field]),field,rg['submitter_read_group_id'])) metadata_dict['read_groups'].append(rg) @@ -262,7 +274,7 @@ def main(metadata,url,bam_from_cram,bam_from_cram_reference,recalculate_size_and optional_experimental_fields.remove("rin") for optional_experimental_field in optional_experimental_fields: - if metadata.get(optional_experimental_field): + if optional_experimental_field in metadata.keys(): payload['experiment'][optional_experimental_field]=metadata.get(optional_experimental_field) # Int optional_experimental_fields=["rin"] @@ -274,6 +286,12 @@ def main(metadata,url,bam_from_cram,bam_from_cram_reference,recalculate_size_and if metadata.get('experimental_strategy')=='RNA-Seq' and not metadata.get("library_strandedness"): sys.exit(f"'experimental_strategy' 'RNA-Seq' specified but 'library_strandedness' is missing. Resubmit with both values 'experimental_strategy' and 'library_strandedness'") + # Targetted Sequencing : + if metadata.get('experimental_strategy')=="Targeted-Seq" or metadata.get('experimental_strategy')=="WXS": + for field in ['target_capture_kit','primary_target_regions','capture_target_regions']: + if field not in metadata.keys(): + sys.exit(f"'experimental_strategy' '%s' specified but '%s' is missing. Resubmit with both values 'experimental_strategy' and '%s'" % (metadata.get('experimental_strategy'),field,field)) + # get sample of the payload sample = { 'submitterSampleId': metadata.get('submitter_sample_id'), @@ -449,4 +467,4 @@ def main(metadata,url,bam_from_cram,bam_from_cram_reference,recalculate_size_and extra_info[row_type][row_id][row_field]=row_val - main(metadata,url,args.bam_from_cram,args.bam_from_cram_reference,args.recalculate_size_and_md5_files,extra_info) \ No newline at end of file + main(metadata,url,args.bam_from_cram,args.bam_from_cram_reference,args.recalculate_size_and_md5_files,extra_info) diff --git a/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/nextflow.config b/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/nextflow.config similarity index 100% rename from wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/nextflow.config rename to wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/nextflow.config diff --git a/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/pkg.json b/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/pkg.json similarity index 97% rename from wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/pkg.json rename to wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/pkg.json index 6fd6c9d..6898e85 100644 --- a/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/pkg.json +++ b/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/pkg.json @@ -1,6 +1,6 @@ { "name": "payload-gen-seq-experiment", - "version": "0.8.2", + "version": "0.8.3", "description": "SONG payload generation for sequencing experiment", "main": "main.nf", "deprecated": false, diff --git a/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/wfpr_modules b/wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/wfpr_modules similarity index 100% rename from wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.2/wfpr_modules rename to wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/wfpr_modules diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1/.dockerignore b/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/.dockerignore similarity index 100% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1/.dockerignore rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/.dockerignore diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1/Dockerfile b/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/Dockerfile similarity index 100% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1/Dockerfile rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/Dockerfile diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1/README.md b/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/README.md similarity index 100% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1/README.md rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/README.md diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1/main.nf b/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/main.nf similarity index 99% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1/main.nf rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/main.nf index 84f1935..a34b31b 100755 --- a/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1/main.nf +++ b/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/main.nf @@ -24,7 +24,7 @@ /* this block is auto-generated based on info from pkg.json where */ /* changes can be made if needed, do NOT modify this block manually */ nextflow.enable.dsl = 2 -version = '0.1.1' +version = '0.1.2' container = [ 'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.payload-json-to-tsvs' diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1/main.py b/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/main.py similarity index 96% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1/main.py rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/main.py index 2ae9c1d..27005d4 100755 --- a/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1/main.py +++ b/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/main.py @@ -84,9 +84,9 @@ def make_experiment_tsv(metadata): for field in [ 'submitter_sequencing_experiment_id','sequencing_center', 'platform', 'platform_model','experimental_strategy', 'sequencing_date', - "library_isolation_protocol","library_preparation_kit", - "library_strandedness","rin","dv200","spike_ins_included","spike_ins_fasta", - "spike_ins_concentration","target_capture_kit"]: + "library_preparation_kit","library_strandedness","rin","dv200", + "primary_target_regions","capture_target_regions","number_of_genes", + "gene_padding","coverage","target_capture_kit"]: return_metadata[field]=metadata['experiment'].get(field) if metadata['experiment'].get(field) else None return_metadata['program_id']=metadata.get("studyId") diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1/nextflow.config b/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/nextflow.config similarity index 100% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1/nextflow.config rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/nextflow.config diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1/pkg.json b/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/pkg.json similarity index 97% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1/pkg.json rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/pkg.json index 1dfebc6..f6e2306 100644 --- a/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1/pkg.json +++ b/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/pkg.json @@ -1,6 +1,6 @@ { "name": "payload-json-to-tsvs", - "version": "0.1.1", + "version": "0.1.2", "description": "Converts JSON payload to 3 TSVs : Experiment,Files,Read groups", "main": "main.nf", "deprecated": false, diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1/wfpr_modules b/wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/wfpr_modules similarity index 100% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.1/wfpr_modules rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/wfpr_modules From 743e2de08875ff058597624d354e6823ff48cae2 Mon Sep 17 00:00:00 2001 From: edsu7 <22638361+edsu7@users.noreply.github.com> Date: Fri, 9 Jun 2023 13:35:34 -0400 Subject: [PATCH 4/7] bump to override last comment --- argo-data-submission-wf/tests/input/experiment-fq.badWXS.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/argo-data-submission-wf/tests/input/experiment-fq.badWXS.tsv b/argo-data-submission-wf/tests/input/experiment-fq.badWXS.tsv index 781ba0b..5f4df99 100644 --- a/argo-data-submission-wf/tests/input/experiment-fq.badWXS.tsv +++ b/argo-data-submission-wf/tests/input/experiment-fq.badWXS.tsv @@ -1,2 +1,2 @@ type submitter_sequencing_experiment_id program_id submitter_donor_id submitter_specimen_id submitter_sample_id submitter_matched_normal_sample_id sequencing_center platform platform_model experimental_strategy sequencing_date read_group_count -sequencing_experiment SubWf_exp_02_FASTQ_input TEST-QA SubWf_test_01 SubWf_test_01_SP_T SubWf_test_01_SA_T SubWf_test_01_SA_N EXT ILLUMINA HiSeq 2000 WXS 2014-12-12 3 \ No newline at end of file +sequencing_experiment SubWf_exp_02_FASTQ_input TEST-QA SubWf_test_01 SubWf_test_01_SP_T SubWf_test_01_SA_T SubWf_test_01_SA_N EXT ILLUMINA HiSeq 2000 WXS 2014-12-11 3 From eda3c1f1e9586d851a682fe22a01ccfebb004641 Mon Sep 17 00:00:00 2001 From: edsu7 <22638361+edsu7@users.noreply.github.com> Date: Mon, 12 Jun 2023 12:17:47 -0400 Subject: [PATCH 5/7] addressing PR#76 --- argo-data-submission-wf/main.nf | 14 ++++++-------- nextflow.config | 4 ---- 2 files changed, 6 insertions(+), 12 deletions(-) diff --git a/argo-data-submission-wf/main.nf b/argo-data-submission-wf/main.nf index 101d3c6..1b6fad2 100755 --- a/argo-data-submission-wf/main.nf +++ b/argo-data-submission-wf/main.nf @@ -41,12 +41,12 @@ params.cleanup = true // ArgoDataSubmissionWf params.study_id="" params.download_mode="local" -params.song_container = "" -params.song_container_version = "" -params.score_container = "" -params.score_container_version = "" -params.score_mem = 2 -params.score_cpus = 4 +params.song_container = "ghcr.io/overture-stack/song-client" +params.song_container_version = "latest" +params.score_container = "ghcr.io/overture-stack/score" +params.score_container_version = "latest" +params.score_mem = 20 +params.score_cpus = 8 params.score_force = false // sanityChecks @@ -133,8 +133,6 @@ egaDownload_params = [ upload_params = [ 'max_retries': params.max_retries, 'first_retry_wait_time': params.first_retry_wait_time, - 'cpus': params.cpus, - 'mem': params.mem, 'score_force' : params.score_force, 'score_cpus' : params.score_cpus, 'score_mem' : params.score_mem, diff --git a/nextflow.config b/nextflow.config index b39f351..bcf5649 100644 --- a/nextflow.config +++ b/nextflow.config @@ -45,10 +45,6 @@ process { cpus = 2 memory = 2.GB } - withName: scoreUpload { - cpus = 4 - memory = 10.GB - } withName: songPublish { cpus = 2 memory = 2.GB From 3eba607fcaf362bfb3eb49b6b1ae93658062259a Mon Sep 17 00:00:00 2001 From: edsu7 <22638361+edsu7@users.noreply.github.com> Date: Tue, 13 Jun 2023 13:18:49 -0400 Subject: [PATCH 6/7] switch to static container versions --- argo-data-submission-wf/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/argo-data-submission-wf/main.nf b/argo-data-submission-wf/main.nf index 1b6fad2..b35eeb3 100755 --- a/argo-data-submission-wf/main.nf +++ b/argo-data-submission-wf/main.nf @@ -42,9 +42,9 @@ params.cleanup = true params.study_id="" params.download_mode="local" params.song_container = "ghcr.io/overture-stack/song-client" -params.song_container_version = "latest" +params.song_container_version = "5.0.2" params.score_container = "ghcr.io/overture-stack/score" -params.score_container_version = "latest" +params.score_container_version = "5.9.0" params.score_mem = 20 params.score_cpus = 8 params.score_force = false From 970cf89849c0df15a81034364c7a5fb524c0e018 Mon Sep 17 00:00:00 2001 From: edsu7 <22638361+edsu7@users.noreply.github.com> Date: Tue, 27 Jun 2023 13:14:17 -0400 Subject: [PATCH 7/7] add new `sanity-check` and `validate-seqtools` versions --- argo-data-submission-wf/main.nf | 4 +-- argo-data-submission-wf/pkg.json | 4 +-- .../tests/input/experiment-fq.badWXS2.tsv | 2 ++ .../local-test-job-16-WXSmissingMatched.json | 8 +++++ .../.dockerignore | 0 .../Dockerfile | 0 .../README.md | 0 .../main.nf | 2 +- .../main.py | 34 +++++++++++++++++-- .../nextflow.config | 0 .../pkg.json | 2 +- .../wfpr_modules | 0 .../.dockerignore | 0 .../Dockerfile | 2 +- .../README.md | 0 .../main.nf | 2 +- .../main.py | 0 .../nextflow.config | 0 .../pkg.json | 2 +- .../wfpr_modules | 0 20 files changed, 50 insertions(+), 12 deletions(-) create mode 100644 argo-data-submission-wf/tests/input/experiment-fq.badWXS2.tsv create mode 100644 argo-data-submission-wf/tests/local-test-job-16-WXSmissingMatched.json rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{sanity-check@0.1.1 => sanity-check@0.1.3}/.dockerignore (100%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{sanity-check@0.1.1 => sanity-check@0.1.3}/Dockerfile (100%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{sanity-check@0.1.1 => sanity-check@0.1.3}/README.md (100%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{sanity-check@0.1.1 => sanity-check@0.1.3}/main.nf (99%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{sanity-check@0.1.1 => sanity-check@0.1.3}/main.py (87%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{sanity-check@0.1.1 => sanity-check@0.1.3}/nextflow.config (100%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{sanity-check@0.1.1 => sanity-check@0.1.3}/pkg.json (97%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{sanity-check@0.1.1 => sanity-check@0.1.3}/wfpr_modules (100%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{validate-seqtools@0.1.7 => validate-seqtools@0.1.8}/.dockerignore (100%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{validate-seqtools@0.1.7 => validate-seqtools@0.1.8}/Dockerfile (99%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{validate-seqtools@0.1.7 => validate-seqtools@0.1.8}/README.md (100%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{validate-seqtools@0.1.7 => validate-seqtools@0.1.8}/main.nf (99%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{validate-seqtools@0.1.7 => validate-seqtools@0.1.8}/main.py (100%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{validate-seqtools@0.1.7 => validate-seqtools@0.1.8}/nextflow.config (100%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{validate-seqtools@0.1.7 => validate-seqtools@0.1.8}/pkg.json (97%) rename wfpr_modules/github.com/icgc-argo/argo-data-submission/{validate-seqtools@0.1.7 => validate-seqtools@0.1.8}/wfpr_modules (100%) diff --git a/argo-data-submission-wf/main.nf b/argo-data-submission-wf/main.nf index b35eeb3..4ced546 100755 --- a/argo-data-submission-wf/main.nf +++ b/argo-data-submission-wf/main.nf @@ -165,13 +165,13 @@ submissionReceipt_params = [ ] include { SongScoreUpload as uploadWf } 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 { validateSeqtools as valSeq} from './wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/main.nf' params(validateSeq_params) +include { validateSeqtools as valSeq} from './wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/main.nf' params(validateSeq_params) include { EgaDownloadWf as egaWf } from './wfpr_modules/github.com/icgc-argo/argo-data-submission/ega-download-wf@0.1.6/main.nf' params(egaDownload_params) include { payloadGenSeqExperiment as pGenExp} from './wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/main.nf' params(payloadGen_params) include { cleanupWorkdir as cleanup } from './wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/cleanup-workdir@1.0.0.1/main.nf' include { cram2bam } from './wfpr_modules/github.com/icgc-argo-workflows/dna-seq-processing-tools/cram2bam@0.1.0/main.nf' params(cram2bam_params) include { getSecondaryFiles } from './wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/helper-functions@1.0.1.1/main.nf' params([*:params, 'cleanup': false]) -include { sanityCheck } from './wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/main.nf' params(sanityCheck_params) +include { sanityCheck } from './wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3/main.nf' params(sanityCheck_params) include { payloadJsonToTsvs } from './wfpr_modules/github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2/main.nf' params(payloadJsonToTsvs_params) include { submissionReceipt } from './wfpr_modules/github.com/icgc-argo/argo-data-submission/submission-receipt@0.1.0/main.nf' params(submissionReceipt_params) // please update workflow code as needed diff --git a/argo-data-submission-wf/pkg.json b/argo-data-submission-wf/pkg.json index 79e75bf..3bad6c8 100644 --- a/argo-data-submission-wf/pkg.json +++ b/argo-data-submission-wf/pkg.json @@ -12,13 +12,13 @@ "url": "https://github.com/icgc-argo/argo-data-submission.git" }, "dependencies": [ - "github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7", + "github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8", "github.com/icgc-argo/argo-data-submission/ega-download-wf@0.1.6", "github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3", "github.com/icgc-argo-workflows/data-processing-utility-tools/cleanup-workdir@1.0.0.1", "github.com/icgc-argo-workflows/dna-seq-processing-tools/cram2bam@0.1.0", "github.com/icgc-argo/argo-data-submission/payload-json-to-tsvs@0.1.2", - "github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1", + "github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3", "github.com/icgc-argo/argo-data-submission/submission-receipt@0.1.0", "github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3" ], diff --git a/argo-data-submission-wf/tests/input/experiment-fq.badWXS2.tsv b/argo-data-submission-wf/tests/input/experiment-fq.badWXS2.tsv new file mode 100644 index 0000000..697bee1 --- /dev/null +++ b/argo-data-submission-wf/tests/input/experiment-fq.badWXS2.tsv @@ -0,0 +1,2 @@ +type submitter_sequencing_experiment_id program_id submitter_donor_id submitter_specimen_id submitter_sample_id submitter_matched_normal_sample_id sequencing_center platform platform_model experimental_strategy sequencing_date read_group_count target_capture_kit primary_target_regions capture_target_regions +sequencing_experiment SubWf_exp_02_FASTQ_input TEST-QA SubWf_test_01 SubWf_test_01_SP_T SubWf_test_01_SA_T SubWf_tes EXT ILLUMINA HiSeq 2000 WXS 2014-12-12 3 dummy_val dummy_val dummy_val diff --git a/argo-data-submission-wf/tests/local-test-job-16-WXSmissingMatched.json b/argo-data-submission-wf/tests/local-test-job-16-WXSmissingMatched.json new file mode 100644 index 0000000..d9f3cf1 --- /dev/null +++ b/argo-data-submission-wf/tests/local-test-job-16-WXSmissingMatched.json @@ -0,0 +1,8 @@ +{ + "study_id": "TEST-QA", + "experiment_info_tsv": "input/experiment-fq.badWXS2.tsv", + "read_group_info_tsv": "input/read_group-fq.v2.tsv", + "file_info_tsv": "input/file-fq.v2.tsv", + "download_mode": "local", + "publish_dir": "outdir" +} diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/.dockerignore b/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3/.dockerignore similarity index 100% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/.dockerignore rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3/.dockerignore diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/Dockerfile b/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3/Dockerfile similarity index 100% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/Dockerfile rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3/Dockerfile diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/README.md b/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3/README.md similarity index 100% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/README.md rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3/README.md diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/main.nf b/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3/main.nf similarity index 99% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/main.nf rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3/main.nf index 3709e40..b4be6eb 100755 --- a/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/main.nf +++ b/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3/main.nf @@ -24,7 +24,7 @@ /* this block is auto-generated based on info from pkg.json where */ /* changes can be made if needed, do NOT modify this block manually */ nextflow.enable.dsl = 2 -version = '0.1.1' +version = '0.1.3' container = [ 'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.sanity-check' diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/main.py b/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3/main.py similarity index 87% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/main.py rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3/main.py index b5f3fbe..c832a13 100755 --- a/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/main.py +++ b/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3/main.py @@ -58,7 +58,7 @@ def main(): args.clinical_url, args.api_token ) - + final_metadata=compile_metadata( metadata, clinical_metadata @@ -67,6 +67,7 @@ def main(): final_metadata, args.submission_song_url ) + if not args.force: check_analysis_exists( final_metadata, @@ -74,7 +75,7 @@ def main(): ) update_tsv(final_metadata,"updated_"+args.experiment_info_tsv) - + def load_tsv(experiment_info_tsv): metadata_dict = {} @@ -145,12 +146,39 @@ def get_clinical(metadata,clinical_url,api_token): sample_ind=[ele for ele,sample in enumerate(response.json()['specimens'][specimen_ind[0]]['samples']) if sample['sampleId']==return_metadata['sample_id']] if len(sample_ind)!=1: - sys.exit("ID Mismatch detected. Sample_id:'%s'/'%s' was not found within Specimen:'%s'/'%s' 's samples" % (metadata['submitter_sample_id'],return_metadata['sample_id'],metadata['submitter_specimen_id'],return_metadata['specimen_id'],)) + sys.exit("ID Mismatch detected. Sample_id:'%s'/'%s' was not found within Specimen:'%s'/'%s' 's samples" % (metadata['submitter_sample_id'],return_metadata['sample_id'],metadata['submitter_specimen_id'],return_metadata['specimen_id'])) return_metadata['sample_type']=response.json()['specimens'][specimen_ind[0]]['samples'][sample_ind[0]]['sampleType'] return_metadata['submitter_sample_id']=response.json()['specimens'][specimen_ind[0]]['samples'][sample_ind[0]]['submitterId'] + if return_metadata['tumour_normal_designation']=="Tumour": + #WGS, WXS, RNA-Seq, Bisulfite-Seq, ChIP-Seq, Targeted-Seq + if metadata.get("submitter_matched_normal_sample_id"): + check_normal_sample_exists(metadata,response.json()) + else: + if metadata.get("experimental_strategy") in ['WGS','WXS']: + sys.exit("Null entry for `submitter_matched_normal_sample_id` detected. For tumour `experiment_strategy` type %s ,this field is required and must reference a registered normal sample." % (metadata.get("experimental_strategy"))) + return return_metadata + + +def check_normal_sample_exists(metadata,clinical_metadata): + submitter_id=metadata['submitter_matched_normal_sample_id'] + + return_id=None + tumourNormalDesignation=None + + for specimen in clinical_metadata['specimens']: + for samples in specimen['samples']: + if samples['submitterId']==submitter_id: + return_id=samples['submitterId'] + tumourNormalDesignation=specimen["tumourNormalDesignation"] + if return_id==None: + sys.exit("'submitter_matched_normal_sample_id':%s was not found in study. Please verify '%s' has been registered." % (submitter_id,submitter_id)) + if tumourNormalDesignation=="Tumour": + sys.exit("'submitter_matched_normal_sample_id':%s detected as tumour instead of normal. Please verify correct sample." % (submitter_id)) + + def compile_metadata(metadata,clinical_metadata): ###Over-write metadata with clinical_metadata diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/nextflow.config b/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3/nextflow.config similarity index 100% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/nextflow.config rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3/nextflow.config diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/pkg.json b/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3/pkg.json similarity index 97% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/pkg.json rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3/pkg.json index a700cc4..f4ed9cf 100644 --- a/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/pkg.json +++ b/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3/pkg.json @@ -1,6 +1,6 @@ { "name": "sanity-check", - "version": "0.1.1", + "version": "0.1.3", "description": "Data submission sanity checks including verifying info from Clinical API", "main": "main.nf", "deprecated": false, diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/wfpr_modules b/wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3/wfpr_modules similarity index 100% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.1/wfpr_modules rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3/wfpr_modules diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/.dockerignore b/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/.dockerignore similarity index 100% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/.dockerignore rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/.dockerignore diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/Dockerfile b/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/Dockerfile similarity index 99% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/Dockerfile rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/Dockerfile index 3b72eb9..bc9fcef 100644 --- a/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/Dockerfile +++ b/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/Dockerfile @@ -37,7 +37,7 @@ RUN cd /tmp &&\ # Install seq-tools -RUN pip install git+https://github.com/icgc-argo/seq-tools.git@1.2.4 +RUN pip install git+https://github.com/icgc-argo/seq-tools.git@1.2.5 #RUN git clone https://github.com/icgc-argo/seq-tools.git@1.1.0 &&\ # git clone https://github.com/icgc-argo/seq-tools.git@1.1.0 # cd seq-tools &&\ diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/README.md b/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/README.md similarity index 100% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/README.md rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/README.md diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/main.nf b/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/main.nf similarity index 99% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/main.nf rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/main.nf index cf11e27..56a1cc9 100755 --- a/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/main.nf +++ b/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/main.nf @@ -25,7 +25,7 @@ /* this block is auto-generated based on info from pkg.json where */ /* changes can be made if needed, do NOT modify this block manually */ nextflow.enable.dsl = 2 -version = '0.1.7' +version = '0.1.8' container = [ 'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.validate-seqtools' diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/main.py b/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/main.py similarity index 100% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/main.py rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/main.py diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/nextflow.config b/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/nextflow.config similarity index 100% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/nextflow.config rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/nextflow.config diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/pkg.json b/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/pkg.json similarity index 97% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/pkg.json rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/pkg.json index a75f6a7..2800b08 100644 --- a/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/pkg.json +++ b/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/pkg.json @@ -1,6 +1,6 @@ { "name": "validate-seqtools", - "version": "0.1.7", + "version": "0.1.8", "description": "Using Seq-tools, validates molecular", "main": "main.nf", "deprecated": false, diff --git a/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/wfpr_modules b/wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/wfpr_modules similarity index 100% rename from wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.7/wfpr_modules rename to wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/wfpr_modules