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Merge pull request #18 from icgc-argo-workflows/sanger-wxs-variant-calling@3.1.6-3.7.0
[release]
2 parents 7b77703 + 3805c67 commit 657a804

25 files changed

Lines changed: 179 additions & 85 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"
27+
env:
28+
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
84-
uses: actions/setup-python@v2
86+
- name: Set up Python 3.10
87+
uses: actions/setup-python@v3
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with:
86-
python-version: 3.6
89+
python-version: "3.10"
90+
architecture: "x64"
91+
env:
92+
AGENT_TOOLSDIRECTORY: /opt/hostedtoolcache
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- name: Install dependencies
8995
run: |
@@ -177,6 +183,8 @@ jobs:
177183
body: |
178184
* 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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2,4 +2,4 @@ project_name: sanger-wxs-variant-calling
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license: GNU Affero General Public License v3
33
repo_type: git
44
repo_server: github.com
5-
repo_account: icgc-argo
5+
repo_account: icgc-argo-workflows

‎sanger-wxs-variant-calling/main.nf‎

Lines changed: 40 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
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nextflow.enable.dsl = 2
33
name = 'sanger-wxs-variant-calling'
44
short_name = 'sanger-wxs'
5-
version = '3.1.6-3.6.0'
5+
version = '3.1.6-3.7.0'
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77

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/*
@@ -119,17 +119,24 @@ params.normal_extra_info = "NO_FILE6"
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120120
// dir for outputs, must be set when running in local mode
121121
params.publish_dir = ""
122-
123-
params.api_token = ""
124-
params.song_url = ""
125-
params.score_url = ""
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params.cleanup = true
127-
128123
params.cpus = 1
129124
params.mem = 1
130125
params.max_retries = 5 // set to 0 will disable retry
131126
params.first_retry_wait_time = 1 // in seconds
132127

128+
// song/score setting
129+
params.song_url = ""
130+
params.song_container = "ghcr.io/overture-stack/song-client"
131+
params.song_container_version = "5.0.2"
132+
params.score_url = ""
133+
params.score_container = "ghcr.io/overture-stack/score"
134+
params.score_container_version = "5.9.0"
135+
params.score_mem = 20
136+
params.score_cpus = 8
137+
params.score_force = false
138+
params.api_token = ""
139+
133140
params.download = [:]
134141
params.generateBas = [:]
135142
params.sangerWxsVariantCaller = [:]
@@ -145,7 +152,16 @@ download_params = [
145152
'max_retries': params.max_retries,
146153
'first_retry_wait_time': params.first_retry_wait_time,
147154
'song_url': params.song_url,
155+
'song_container': params.song_container,
156+
'song_container_version': params.song_container_version,
157+
'song_cpus': params.cpus,
158+
'song_mem': params.mem,
148159
'score_url': params.score_url,
160+
'score_container': params.score_container,
161+
'score_container_version': params.score_container_version,
162+
'score_cpus' : params.score_cpus,
163+
'score_mem' : params.score_mem,
164+
'score_transport_mem' : params.score_mem,
149165
'api_token': params.api_token,
150166
*:(params.download ?: [:])
151167
]
@@ -205,29 +221,36 @@ payloadGenVariantCall_params = [
205221
]
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207223
upload_params = [
208-
'cpus': params.cpus,
209-
'mem': params.mem,
210224
'max_retries': params.max_retries,
211-
'publish_dir': params.publish_dir,
212225
'first_retry_wait_time': params.first_retry_wait_time,
213226
'song_url': params.song_url,
227+
'song_container': params.song_container,
228+
'song_container_version': params.song_container_version,
229+
'song_cpus': params.cpus,
230+
'song_mem': params.mem,
214231
'score_url': params.score_url,
232+
'score_container': params.score_container,
233+
'score_container_version': params.score_container_version,
234+
'score_force' : params.score_force,
235+
'score_cpus' : params.score_cpus,
236+
'score_mem' : params.score_mem,
237+
'score_transport_mem' : params.score_mem,
215238
'api_token': params.api_token,
216-
*:(params.uploadVariant ?: [:])
239+
*:(params.upload ?: [:])
217240
]
218241

219242

220243
// Include all modules and pass params
221-
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)
244+
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)
222245
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)
223246
include { sangerWxsVariantCaller as sangerWxs } from './modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/sanger-wxs-variant-caller.3.1.6-3/tools/sanger-wxs-variant-caller/sanger-wxs-variant-caller.nf' params(sangerWxsVariantCaller_params)
224247
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)
225248
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)
226249
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)
227250
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)
228251
include { extractFilesFromTarball as extractVarSnv; extractFilesFromTarball as extractVarIndel; extractFilesFromTarball as extractQC } 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)
229-
include { payloadGenVariantCalling as pGenVarSnv; payloadGenVariantCalling as pGenVarIndel; 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" params(payloadGenVariantCall_params)
230-
include { SongScoreUpload as upSnv; SongScoreUpload as upIndel; 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)
252+
include { payloadGenVariantCalling as pGenVarSnv; payloadGenVariantCalling as pGenVarIndel; 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" params(payloadGenVariantCall_params)
253+
include { SongScoreUpload as upSnv; SongScoreUpload as upIndel; 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)
231254
include { cleanupWorkdir as cleanup } from './wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/cleanup-workdir@1.0.0/main'
232255
include { getSecondaryFiles } from './wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.0/main'
233256
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'
@@ -358,10 +381,10 @@ workflow SangerWxs {
358381

359382
// upload variant results in paralllel
360383
if (!local_mode) {
361-
upSnv(study_id, pGenVarSnv.out.payload, pGenVarSnv.out.files_to_upload)
362-
upIndel(study_id, pGenVarIndel.out.payload, pGenVarIndel.out.files_to_upload)
363-
upSupp(study_id, pGenVarSupp.out.payload, pGenVarSupp.out.files_to_upload)
364-
upQc(study_id, pGenQc.out.payload, pGenQc.out.files_to_upload)
384+
upSnv(study_id, pGenVarSnv.out.payload, pGenVarSnv.out.files_to_upload, '')
385+
upIndel(study_id, pGenVarIndel.out.payload, pGenVarIndel.out.files_to_upload, '')
386+
upSupp(study_id, pGenVarSupp.out.payload, pGenVarSupp.out.files_to_upload, '')
387+
upQc(study_id, pGenQc.out.payload, pGenQc.out.files_to_upload, '')
365388
}
366389

367390
if (params.cleanup) {

‎sanger-wxs-variant-calling/pkg.json‎

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@@ -1,6 +1,6 @@
11
{
22
"name": "sanger-wxs-variant-calling",
3-
"version": "3.1.6-3.6.0",
3+
"version": "3.1.6-3.7.0",
44
"description": "ICGC ARGO Sanger WXS Variant Calling Workflow",
55
"main": "main.nf",
66
"deprecated": false,
@@ -11,15 +11,15 @@
1111
],
1212
"repository": {
1313
"type": "git",
14-
"url": "https://github.com/icgc-argo/sanger-wxs-variant-calling.git"
14+
"url": "https://github.com/icgc-argo-workflows/sanger-wxs-variant-calling.git"
1515
},
1616
"dependencies": [
17-
"github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.6.0",
17+
"github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-variant-calling@0.7.0",
1818
"github.com/icgc-argo/data-processing-utility-tools/payload-add-uniform-ids@0.1.1",
1919
"github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.0",
2020
"github.com/icgc-argo/data-processing-utility-tools/cleanup-workdir@1.0.0",
21-
"github.com/icgc-argo/nextflow-data-processing-utility-tools/song-score-download@2.6.1",
22-
"github.com/icgc-argo/nextflow-data-processing-utility-tools/song-score-upload@2.6.1"
21+
"github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-download@2.9.0",
22+
"github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3"
2323
],
2424
"devDependencies": [],
2525
"contributors": [
@@ -31,6 +31,6 @@
3131
}
3232
],
3333
"license": "GNU Affero General Public License v3",
34-
"bugReport": "https://github.com/icgc-argo/sanger-wxs-variant-calling/issues",
35-
"homepage": "https://github.com/icgc-argo/sanger-wxs-variant-calling#readme"
34+
"bugReport": "https://github.com/icgc-argo-workflows/sanger-wxs-variant-calling/issues",
35+
"homepage": "https://github.com/icgc-argo-workflows/sanger-wxs-variant-calling#readme"
3636
}

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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Original file line numberDiff line numberDiff line change
@@ -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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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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