release 1.0.0 #16

HomoPolyethylen · 2024-09-12T15:22:04Z

PR checklist

Signed-off-by: SusiJo <susanne.jodoin@gmx.de>

Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>

… into querynator_module

This reverts commit 4b4c3eb.

Merge pull request #7 from HomoPolyethylen/template-merge

* feat!: specify cancer type for cgi & civic in samplesheet (#5) * refactored meta info parsing * bumped querynator to 0.5.1 moved cancer type from params to samplesheet * updated usage * updated usage * lint * update bcftools/norm to 1.18 * update bcftools/view to 1.18 * updated gunzip module * updated custom/dumpsoftwareversions module * updated utils_nfcore_pipeline subworkflow * lint * added cancer type defaults * updated module gunzip * updated module tabix/tabix * updated module tabix/bgziptabix * bump querynator to 0.5.4 * docs: update CHANGELOG * fix: disable parallelization for QUERYCGI CGI blocks multiple parallel requests to their API fixes #10 * build: bump version to 1.0.0 * test: run multiple samples for the full test * Bump querynator 0.5.5 * chore: remove obsolete TODOs * chore: update nf-core modules * chore: update nf-core subworkflows * chore(querynator): update to 0.5.5 * fix(docs): fix github actions badges

github-actions · 2024-09-12T15:23:42Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 5129696

+| ✅ 177 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.0.0
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

files_unchanged - File ignored due to lint config: assets/nf-core-variantmtb_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-variantmtb_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-variantmtb_logo_dark.png

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-variantmtb_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-variantmtb_logo_light.png
files_exist - File found: docs/images/nf-core-variantmtb_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-variantmtb_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowVariantmtb.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.outdir= results
nextflow_config - Config default value correct: params.databases= cgi, civic
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.tracedir= results/pipeline_info
nextflow_config - Config default value correct: params.validate_params= true
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (147 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: ci.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - BCFTOOLS_NORM found in conf/modules.config and Nextflow scripts.
modules_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
modules_config - QUERYNATOR_CGIAPI found in conf/modules.config and Nextflow scripts.
modules_config - QUERYNATOR_CIVICAPI found in conf/modules.config and Nextflow scripts.
modules_config - QUERYNATOR_CREATEREPORT found in conf/modules.config and Nextflow scripts.
modules_config - TABIX_TABIX found in conf/modules.config and Nextflow scripts.
modules_config - TABIX_BGZIPTABIX found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-09-12 15:23:22

HomoPolyethylen · 2024-09-12T16:06:36Z

gh action download and run pipeline fails.
claims, that test file does not exist:

ERROR ~ ERROR: Validation of 'input' file failed!

 -- Check '.nextflow.log' file for details
The following errors have been detected:

* -- Entry 1 - filename: the file or directory 'tests/test_files/test.vcf' does not exist.

but validated existence of test.vcf in previous step (file was correctly printed after tree ./variantmtb run):
https://github.com/qbic-pipelines/variantmtb/actions/runs/10833856860/job/30063333840#step:8:640

feat: add civic evidence filters

mapo9 · 2024-10-11T08:09:54Z

LICENSE

@@ -1,6 +1,6 @@
 MIT License

-Copyright (c) SusiJo
+Copyright (c) SusiJo, mapo9, HomoPolyethylen


🎉 🎉 🎉 🎉

SusiJo and others added 30 commits August 12, 2022 09:16

update description

c3a89ff

test verified commit

9f94ccf

test signed commit

a71e068

adjust samplesheet

4cd7908

include bcftools for pass filtering

ea062aa

added bcftools_split

1277e9b

Signed-off-by: SusiJo <susanne.jodoin@gmx.de>

first draft of querynator module

ffa6fb1

querynator module built and tested

dc4e19b

started to incorporate querynator in pipeline

4d1f352

first draft of incorporated querynator/query_cgi

8b2d012

cgi query running

7fa7391

cancer type fixed

4be11df

made unzipping possible for cgi

45ee490

cgi + first draft civic

397ec75

all done, first draft

c962040

Update nextflow.config

f9ff523

Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>

Update bin/check_samplesheet.py

0bf8355

Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>

next try

640f649

Update bin/check_samplesheet.py

531b7f6

Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>

Update bin/check_samplesheet.py

8b4d678

Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>

Update modules/local/querynator/cgiapi.nf

5f82e69

Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>

Update workflows/variantmtb.nf

67ca6c3

Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>

Modules

2847c02

Merge branch 'querynator_module' of https://github.com/mapo9/variantmtb…

f491efe

… into querynator_module

some changes

ee8053b

querynator update

cd2a485

querynator updated

3baa95a

docs added

ad2c642

docs added

9cc6035

remove fastqc

ee47d0b

HomoPolyethylen and others added 17 commits April 3, 2024 20:59

added/updated tests

9c26c08

minor fix

77ec38b

added citations

8758aae

moved fasta channel init to main workflow

eabb511

added link to list of cancer types at querynator repo

ace6da5

added BGZF compressed vcf to full test

a077f4e

refactored

ac69453

prettier

1298803

added enum to genome

7c4c3a8

fixed igenomes and linting

63bf60d

update querynator to 0.4.2

5d780c3

added name to contributors

2acf6f8

removed unused script

1d24e7c

minor adjustments

4b4c3eb

Revert "minor adjustments"

87467df

This reverts commit 4b4c3eb.

Template update for nf-core/tools v2.13.1

f251b7d

Merge pull request #7 from HomoPolyethylen/template-merge

HomoPolyethylen self-assigned this Sep 12, 2024

HomoPolyethylen and others added 7 commits October 10, 2024 19:07

feat: add civic evidence filters

c42ca8c

chore: bump querynator to 0.6.0

0c08ab2

chore: update nf-core modules

50af8d0

chore: update nf-core subworkflows

cc9ab51

docs: update changelog

e40e4d9

docs: add actionability profile

ef73c88

Merge pull request #20 from HomoPolyethylen/civic-filters

b36bc88

feat: add civic evidence filters

HomoPolyethylen requested a review from mapo9 October 11, 2024 07:28

mapo9 approved these changes Oct 11, 2024

View reviewed changes

HomoPolyethylen merged commit 0aa9cf5 into master Oct 11, 2024
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release 1.0.0 #16

release 1.0.0 #16

HomoPolyethylen commented Sep 12, 2024 •

edited

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github-actions bot commented Sep 12, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

HomoPolyethylen commented Sep 12, 2024 •

edited

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mapo9 Oct 11, 2024

release 1.0.0 #16

release 1.0.0 #16

Conversation

HomoPolyethylen commented Sep 12, 2024 • edited Loading

PR checklist

github-actions bot commented Sep 12, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

HomoPolyethylen commented Sep 12, 2024 • edited Loading

mapo9 Oct 11, 2024

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HomoPolyethylen commented Sep 12, 2024 •

edited

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github-actions bot commented Sep 12, 2024 •

edited

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`nf-core lint` overall result: Passed ✅ ⚠️

HomoPolyethylen commented Sep 12, 2024 •

edited

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