Template update for nf-core/tools v2.13.1 #7

HomoPolyethylen · 2024-03-29T21:48:40Z

PR checklist

Changes

performed the template update for nf-core/tools version 2.13.1
added env variable CIVICPY_CACHE_FILE to civicapi module, setting the path for the civicpy cache to workDir/.civicpy/cache.pkl
fixed several linting errors
- reinstalled bcftools/norm
- reinstalled tabix/bgziptabix
- updated bcftools/view
- updated gunzip
- updated custom/dumpsoftwareversions
- updated tabix/tabix
replaced the nf-core logo with the qbic logo. this is the only thing preventing the project from linting completely... but it looks so nice :(

ToDo

discuss, what kind of release this is
modify changelog.md

…nome flag

removed fasta default value, so it can be reassigned by script and ge…

github-actions · 2024-03-29T21:50:04Z

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

Posted for pipeline commit 87467df

+| ✅ 168 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

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 full-sized test dataset and amend the paragraph below if applicable
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
pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output

❔ 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 found: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: .nf-core.yaml
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: .github/workflows/push_dockerhub.yml
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: docs/images/nf-core-variantmtb_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
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/Workflow.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/WorkflowVariantmtb.groovy
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 manifest.version ends in dev: 1.0dev
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.cgi_cancer_type= 'Any cancer type\
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
files_unchanged - pyproject.toml 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 (131 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: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.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' 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'

Run details

nf-core/tools version 2.13.1
Run at 2024-04-09 09:28:54

This reverts commit 5402ddf.

HomoPolyethylen · 2024-04-01T19:31:42Z

finally ✔️ 🚀

HomoPolyethylen · 2024-04-01T19:41:41Z

Issues that are not neatly covered in this PR:

linting logo pngs passes locally but fails on CI:
- logo generation is inconsistent between github actions runners and local execution nf-core/tools#2893
- ignored files to pass linting e1c3f37
modifying subworflows/nf-core/utils_nfcore_pipeline/main.nf to print qbic logo instead of nfcore logo fails linting
- no ingorable linting error provided
- Subworkflow Tests Failed but running subworkflow test (locally) passes (if checksums are updated)
- removed qbic logo for now to pass tests

mapo9

looks great! 🚀
I only have a couple of minor comments.
Also asked jonas to have a look as he did a template update himself recently.
When he did, I will approve 👍

conf/test_full.config

main.nf

modules/local/querynator/civicapi.nf

nextflow_schema.json

subworkflows/local/create_querynator_input.nf

jonasscheid

Couple of minor things, but LGTM in general 🙌🏼

main.nf

nextflow.config

nextflow_schema.json

subworkflows/local/utils_nfcore_variantmtb_pipeline/main.nf

workflows/variantmtb.nf

famosab

I just a some small comments but otherwise LGTM :)

LICENSE

conf/test_full.config

subworkflows/local/utils_nfcore_variantmtb_pipeline/main.nf

This reverts commit 4b4c3eb.

HomoPolyethylen · 2024-04-09T09:32:35Z

5d780c3 fixed issue #8

HomoPolyethylen and others added 8 commits March 5, 2024 13:29

removed fasta default value, so it can be reassigned by script and ge…

4adfd15

…nome flag

Merge pull request #3 from HomoPolyethylen/igenomes

57c5940

removed fasta default value, so it can be reassigned by script and ge…

Merge branch 'qbic-pipelines:dev' into dev

3dec24c

added qbicpipelines header and logo

c65c4a0

Template update for nf-core/tools version 2.13.1

28b2e99

template update 2.13.1

b0993b5

added qbic logo and minor fixes

3c6ab34

nf-core lint

4cde7a8

HomoPolyethylen requested review from famosab and mapo9 March 29, 2024 21:48

HomoPolyethylen self-assigned this Mar 29, 2024

HomoPolyethylen mentioned this pull request Mar 29, 2024

fixed --genome support #6

Closed

10 tasks

HomoPolyethylen added 16 commits March 29, 2024 22:55

prettier

ee3c598

lint

d6b083b

prettier

b391bbc

try ignoring utils_nfcore_pipeline

5402ddf

removed obsolete cgi options and grouped other options

b650c56

Revert "try ignoring utils_nfcore_pipeline"

0a9d810

This reverts commit 5402ddf.

cleanup & description of cgi credentials

3556a54

removed some todos

1692cf1

lint

29845fb

cleanup

eee2195

minor nf-test fix

09fafc2

undo qbicpipelines logo to pass linting

6823605

undo qbicpipelines logo

4ccab48

fixed typo

64de456

fix linting issue by ignoring images

e1c3f37

minor fix

e30d2f1

mapo9 requested changes Apr 3, 2024

View reviewed changes

jonasscheid suggested changes Apr 3, 2024

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HomoPolyethylen added 7 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

jonasscheid approved these changes Apr 4, 2024

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HomoPolyethylen added 3 commits April 4, 2024 13:29

prettier

1298803

added enum to genome

7c4c3a8

fixed igenomes and linting

63bf60d

famosab approved these changes Apr 9, 2024

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mapo9 approved these changes Apr 9, 2024

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HomoPolyethylen added 5 commits April 9, 2024 11:02

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.

HomoPolyethylen merged commit f251b7d into qbic-pipelines:dev Apr 9, 2024
4 checks passed

HomoPolyethylen deleted the template-merge branch April 9, 2024 09:59

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Template update for nf-core/tools v2.13.1 #7

Template update for nf-core/tools v2.13.1 #7

HomoPolyethylen commented Mar 29, 2024 •

edited

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github-actions bot commented Mar 29, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

HomoPolyethylen commented Apr 1, 2024

HomoPolyethylen commented Apr 1, 2024

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famosab left a comment

HomoPolyethylen commented Apr 9, 2024

Template update for nf-core/tools v2.13.1 #7

Template update for nf-core/tools v2.13.1 #7

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HomoPolyethylen commented Mar 29, 2024 • edited Loading

PR checklist

Changes

ToDo

github-actions bot commented Mar 29, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

HomoPolyethylen commented Apr 1, 2024

HomoPolyethylen commented Apr 1, 2024

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HomoPolyethylen commented Apr 9, 2024

HomoPolyethylen commented Mar 29, 2024 •

edited

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github-actions bot commented Mar 29, 2024 •

edited

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