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Merge pull request #16 from icgc-argo-workflows/sanger-wgs-variant-calling@2.1.0-9.7.0
[release]
2 parents 3d4a43b + 48d9057 commit c6b9b42

25 files changed

Lines changed: 762 additions & 42 deletions

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‎.github/workflows/build-test-release.yml‎

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@@ -19,10 +19,13 @@ jobs:
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python 3.6
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uses: actions/setup-python@v2
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- name: Set up Python 3.10
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uses: actions/setup-python@v3
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with:
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python-version: 3.6
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python-version: "3.10"
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architecture: "x64"
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env:
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AGENT_TOOLSDIRECTORY: /opt/hostedtoolcache
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- name: Extract package name and version from branch name
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id: get_pkg_info
@@ -80,10 +83,13 @@ jobs:
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python 3.6
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uses: actions/setup-python@v2
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- name: Set up Python 3.10
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uses: actions/setup-python@v3
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with:
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python-version: 3.6
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python-version: "3.10"
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architecture: "x64"
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env:
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AGENT_TOOLSDIRECTORY: /opt/hostedtoolcache
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- name: Install dependencies
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run: |
@@ -177,6 +183,8 @@ jobs:
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body: |
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* Release `${{ steps.get_pkg_info.outputs.pkg_name }}.v${{ steps.get_pkg_info.outputs.pkg_ver }}` (${{ github.sha }})
179185
* Package `${{ steps.prep_assets.outputs.pkg_tar }}` (sha256: `${{ steps.prep_assets.outputs.pkg_tar_sha }}`)
186+
* Package URI `github.com/${{ needs.build.outputs.repo_lowercase }}/${{ steps.get_pkg_info.outputs.pkg_name }}@${{ steps.get_pkg_info.outputs.pkg_ver }}`
187+
* Run the package: `nextflow run ${{ needs.build.outputs.repo_lowercase }}/${{ steps.get_pkg_info.outputs.pkg_name }}/main.nf -r ${{ steps.get_pkg_info.outputs.pkg_name }}.v${{ steps.get_pkg_info.outputs.pkg_ver }} -params-file <params-json-file>`
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draft: false
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prerelease: false
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‎.wfpm‎

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@@ -2,4 +2,4 @@ project_name: sanger-wgs-variant-calling
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license: GNU Affero General Public License v3
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repo_type: git
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repo_server: github.com
5-
repo_account: icgc-argo
5+
repo_account: icgc-argo-workflows

‎sanger-wgs-variant-calling/main.nf‎

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Original file line numberDiff line numberDiff line change
@@ -2,14 +2,14 @@
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nextflow.preview.dsl=2
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name='sanger-wgs-variant-calling'
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short_name='sanger-wgs'
5-
version = '2.1.0-9.6.0'
5+
version = '2.1.0-9.7.0'
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77
/*
88
========================================================================================
99
ICGC ARGO Sanger WGS Variant Calling Workflow
1010
========================================================================================
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#### Homepage / Documentation
12-
https://github.com/icgc-argo/sanger-wgs-variant-calling
12+
https://github.com/icgc-argo-workflows/sanger-wgs-variant-calling
1313
#### Authors
1414
Junjun Zhang @junjun-zhang <junjun.zhang@oicr.on.ca>
1515
Linda Xiang @lindaxiang <linda.xiang@oicr.on.ca>
@@ -159,16 +159,23 @@ params.normal_extra_info = "NO_FILE6"
159159
// dir for outputs, must be set when running in local mode
160160
params.publish_dir = ""
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params.cleanup = true
162-
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params.api_token = ""
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params.song_url = ""
165-
params.score_url = ""
166-
167162
params.cpus = 1
168163
params.mem = 1
169164
params.max_retries = 5 // set to 0 will disable retry
170165
params.first_retry_wait_time = 1 // in seconds
171166

167+
// song/score setting
168+
params.song_url = ""
169+
params.song_container = "ghcr.io/overture-stack/song-client"
170+
params.song_container_version = "5.0.2"
171+
params.score_url = ""
172+
params.score_container = "ghcr.io/overture-stack/score"
173+
params.score_container_version = "5.9.0"
174+
params.score_mem = 20
175+
params.score_cpus = 8
176+
params.score_force = false
177+
params.api_token = ""
178+
172179
params.download = [:]
173180
params.generateBas = [:]
174181
params.sangerWgsVariantCaller = [:]
@@ -182,12 +189,19 @@ params.upload = [:]
182189
params.extractSangerCall = [:]
183190

184191
download_params = [
185-
'cpus': params.cpus,
186-
'mem': params.mem,
187192
'max_retries': params.max_retries,
188193
'first_retry_wait_time': params.first_retry_wait_time,
189194
'song_url': params.song_url,
195+
'song_container': params.song_container,
196+
'song_container_version': params.song_container_version,
197+
'song_cpus': params.cpus,
198+
'song_mem': params.mem,
190199
'score_url': params.score_url,
200+
'score_container': params.score_container,
201+
'score_container_version': params.score_container_version,
202+
'score_cpus' : params.score_cpus,
203+
'score_mem' : params.score_mem,
204+
'score_transport_mem' : params.score_mem,
191205
'api_token': params.api_token,
192206
*:(params.download ?: [:])
193207
]
@@ -258,28 +272,36 @@ payloadGenVariantCall_params = [
258272
]
259273

260274
upload_params = [
261-
'cpus': params.cpus,
262-
'mem': params.mem,
263275
'max_retries': params.max_retries,
264276
'first_retry_wait_time': params.first_retry_wait_time,
265277
'song_url': params.song_url,
278+
'song_container': params.song_container,
279+
'song_container_version': params.song_container_version,
280+
'song_cpus': params.cpus,
281+
'song_mem': params.mem,
266282
'score_url': params.score_url,
283+
'score_container': params.score_container,
284+
'score_container_version': params.score_container_version,
285+
'score_force' : params.score_force,
286+
'score_cpus' : params.score_cpus,
287+
'score_mem' : params.score_mem,
288+
'score_transport_mem' : params.score_mem,
267289
'api_token': params.api_token,
268290
*:(params.upload ?: [:])
269291
]
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272294
// Include all modules and pass params
273-
include { SongScoreDownload as dnldT; SongScoreDownload as dnldN } from './wfpr_modules/github.com/icgc-argo/nextflow-data-processing-utility-tools/song-score-download@2.6.1/main.nf' params(download_params)
295+
include { SongScoreDownload as dnldT; SongScoreDownload as dnldN } from './wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0/main.nf' params(download_params)
274296
include { generateBas as basT; generateBas as basN; } from './modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/generate-bas.0.2.1.0/tools/generate-bas/generate-bas' params(generateBas_params)
275297
include { sangerWgsVariantCaller as sangerWgs } from './modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/sanger-wgs-variant-caller.2.1.0-9/tools/sanger-wgs-variant-caller/sanger-wgs-variant-caller' params(sangerWgsVariantCaller_params)
276298
include { repackSangerResults as repack } from './modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/repack-sanger-results.0.2.0.0/tools/repack-sanger-results/repack-sanger-results' params(repackSangerResults_params)
277299
include { cavemanVcfFix as cavemanFix } from './modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/caveman-vcf-fix.0.1.0.0/tools/caveman-vcf-fix/caveman-vcf-fix' params(cavemanVcfFix_params)
278300
include { prepSangerSupplement as prepSupp } from './modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/prep-sanger-supplement.0.1.2.0/tools/prep-sanger-supplement/prep-sanger-supplement' params(prepSangerSupplement_params)
279301
include { prepSangerQc as prepQc } from './modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/prep-sanger-qc.0.1.3.0/tools/prep-sanger-qc/prep-sanger-qc' params(prepSangerQc_params)
280302
include { extractFilesFromTarball as extractVarSnv; extractFilesFromTarball as extractVarIndel; extractFilesFromTarball as extractVarCnv; extractFilesFromTarball as extractVarSv } from './modules/raw.githubusercontent.com/icgc-argo/data-processing-utility-tools/extract-files-from-tarball.0.2.0.0/tools/extract-files-from-tarball/extract-files-from-tarball' params(extractSangerCall_params)
281-
include { payloadGenVariantCalling as pGenVarSnv; payloadGenVariantCalling as pGenVarIndel; payloadGenVariantCalling as pGenVarCnv; payloadGenVariantCalling as pGenVarSv; payloadGenVariantCalling as pGenVarSupp; payloadGenVariantCalling as pGenQc } from "./wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.6.0/main.nf" params(payloadGenVariantCall_params)
282-
include { SongScoreUpload as upSnv; SongScoreUpload as upIndel; SongScoreUpload as upCnv; SongScoreUpload as upSv; SongScoreUpload as upQc; SongScoreUpload as upSupp} from './wfpr_modules/github.com/icgc-argo/nextflow-data-processing-utility-tools/song-score-upload@2.6.1/main.nf' params(upload_params)
303+
include { payloadGenVariantCalling as pGenVarSnv; payloadGenVariantCalling as pGenVarIndel; payloadGenVariantCalling as pGenVarCnv; payloadGenVariantCalling as pGenVarSv; payloadGenVariantCalling as pGenVarSupp; payloadGenVariantCalling as pGenQc } from "./wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-variant-calling@0.7.0/main.nf" params(payloadGenVariantCall_params)
304+
include { SongScoreUpload as upSnv; SongScoreUpload as upIndel; SongScoreUpload as upCnv; SongScoreUpload as upSv; SongScoreUpload as upQc; SongScoreUpload as upSupp} from './wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/main.nf' params(upload_params)
283305
include { cleanupWorkdir as cleanup } from './wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/cleanup-workdir@1.0.0/main'
284306
include { getSecondaryFiles } from './wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.0/main'
285307
include { payloadAddUniformIds as pAddIdT; payloadAddUniformIds as pAddIdN } from './wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-add-uniform-ids@0.1.1/main'
@@ -430,12 +452,12 @@ workflow SangerWgs {
430452

431453
// upload variant results
432454
if (!local_mode) {
433-
upSnv(study_id, pGenVarSnv.out.payload, pGenVarSnv.out.files_to_upload)
434-
upIndel(study_id, pGenVarIndel.out.payload, pGenVarIndel.out.files_to_upload)
435-
upCnv(study_id, pGenVarCnv.out.payload, pGenVarCnv.out.files_to_upload)
436-
upSv(study_id, pGenVarSv.out.payload, pGenVarSv.out.files_to_upload)
437-
upSupp(study_id, pGenVarSupp.out.payload, pGenVarSupp.out.files_to_upload)
438-
upQc(study_id, pGenQc.out.payload, pGenQc.out.files_to_upload)
455+
upSnv(study_id, pGenVarSnv.out.payload, pGenVarSnv.out.files_to_upload, '')
456+
upIndel(study_id, pGenVarIndel.out.payload, pGenVarIndel.out.files_to_upload, '')
457+
upCnv(study_id, pGenVarCnv.out.payload, pGenVarCnv.out.files_to_upload, '')
458+
upSv(study_id, pGenVarSv.out.payload, pGenVarSv.out.files_to_upload, '')
459+
upSupp(study_id, pGenVarSupp.out.payload, pGenVarSupp.out.files_to_upload, '')
460+
upQc(study_id, pGenQc.out.payload, pGenQc.out.files_to_upload, '')
439461
}
440462

441463
if (params.cleanup) {

‎sanger-wgs-variant-calling/pkg.json‎

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@@ -1,6 +1,6 @@
11
{
22
"name": "sanger-wgs-variant-calling",
3-
"version": "2.1.0-9.6.0",
3+
"version": "2.1.0-9.7.0",
44
"description": "ICGC ARGO Sanger WGS Variant Calling Workflow",
55
"main": "main.nf",
66
"deprecated": false,
@@ -12,15 +12,15 @@
1212
],
1313
"repository": {
1414
"type": "git",
15-
"url": "https://github.com/icgc-argo/sanger-wgs-variant-calling.git"
15+
"url": "https://github.com/icgc-argo-workflows/sanger-wgs-variant-calling.git"
1616
},
1717
"dependencies": [
18-
"github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.6.0",
18+
"github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-variant-calling@0.7.0",
1919
"github.com/icgc-argo/data-processing-utility-tools/payload-add-uniform-ids@0.1.1",
2020
"github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.0",
2121
"github.com/icgc-argo/data-processing-utility-tools/cleanup-workdir@1.0.0",
22-
"github.com/icgc-argo/nextflow-data-processing-utility-tools/song-score-download@2.6.1",
23-
"github.com/icgc-argo/nextflow-data-processing-utility-tools/song-score-upload@2.6.1"
22+
"github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0",
23+
"github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3"
2424
],
2525
"devDependencies": [],
2626
"contributors": [
@@ -32,6 +32,6 @@
3232
}
3333
],
3434
"license": "GNU Affero General Public License v3",
35-
"bugReport": "https://github.com/icgc-argo/sanger-wgs-variant-calling/issues",
36-
"homepage": "https://github.com/icgc-argo/sanger-wgs-variant-calling#readme"
35+
"bugReport": "https://github.com/icgc-argo-workflows/sanger-wgs-variant-calling/issues",
36+
"homepage": "https://github.com/icgc-argo-workflows/sanger-wgs-variant-calling#readme"
3737
}

wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.6.0/.dockerignore renamed to wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-variant-calling@0.7.0/.dockerignore

File renamed without changes.

wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.6.0/Dockerfile renamed to wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-variant-calling@0.7.0/Dockerfile

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11
FROM python:3.7.9
22

3-
LABEL org.opencontainers.image.source https://github.com/icgc-argo/data-processing-utility-tools
3+
LABEL org.opencontainers.image.source https://github.com/icgc-argo-workflows/data-processing-utility-tools
44

55
RUN groupadd -g 1000 ubuntu && \
66
useradd -l -u 1000 -g ubuntu ubuntu && \

wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.6.0/main.nf renamed to wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-variant-calling@0.7.0/main.nf

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2525
/* this block is auto-generated based on info from pkg.json where */
2626
/* changes can be made if needed, do NOT modify this block manually */
2727
nextflow.enable.dsl = 2
28-
version = '0.6.0'
28+
version = '0.7.0'
2929

3030
container = [
31-
'ghcr.io': 'ghcr.io/icgc-argo/data-processing-utility-tools.payload-gen-variant-calling'
31+
'ghcr.io': 'ghcr.io/icgc-argo-workflows/data-processing-utility-tools.payload-gen-variant-calling'
3232
]
3333
default_container_registry = 'ghcr.io'
3434
/********************************************************************/

wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.6.0/main.py renamed to wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-variant-calling@0.7.0/main.py

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@@ -170,11 +170,13 @@ def get_files_info(file_to_upload, wf_short_name, wf_version, somatic_or_germli
170170
else:
171171
sys.exit('Error: unknown file type "%s"' % file_to_upload)
172172

173+
## Disable the population of qc_metrics into payload to avoid the exposure of sensitive info
173174
tar = tarfile.open(file_to_upload)
174175
for member in tar.getmembers():
175176
if member.name.endswith('.extra_info.json'):
176177
f = tar.extractfile(member)
177178
extra_info = json.load(f)
179+
extra_info.pop('metrics', None)
178180
break
179181
else:
180182
sys.exit('Error: unknown file type "%s"' % file_to_upload)

wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.6.0/nextflow.config renamed to wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-variant-calling@0.7.0/nextflow.config

File renamed without changes.

wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.6.0/pkg.json renamed to wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-variant-calling@0.7.0/pkg.json

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@@ -1,6 +1,6 @@
11
{
22
"name": "payload-gen-variant-calling",
3-
"version": "0.6.0",
3+
"version": "0.7.0",
44
"description": "A tool to generate SONG payloads for variant calling workflows",
55
"main": "main.nf",
66
"deprecated": false,
@@ -11,14 +11,14 @@
1111
],
1212
"repository": {
1313
"type": "git",
14-
"url": "https://github.com/icgc-argo/data-processing-utility-tools.git"
14+
"url": "https://github.com/icgc-argo-workflows/data-processing-utility-tools.git"
1515
},
1616
"container": {
1717
"registries": [
1818
{
1919
"registry": "ghcr.io",
2020
"type": "docker",
21-
"org": "icgc-argo",
21+
"org": "icgc-argo-workflows",
2222
"default": true
2323
}
2424
]
@@ -31,6 +31,6 @@
3131
}
3232
],
3333
"license": "GNU Affero General Public License v3",
34-
"bugReport": "https://github.com/icgc-argo/data-processing-utility-tools/issues",
35-
"homepage": "https://github.com/icgc-argo/data-processing-utility-tools#readme"
34+
"bugReport": "https://github.com/icgc-argo-workflows/data-processing-utility-tools/issues",
35+
"homepage": "https://github.com/icgc-argo-workflows/data-processing-utility-tools#readme"
3636
}

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