Update documentation around VEP and snpEff cache by adamrtalbot · Pull Request #1222 · nf-core/sarek

adamrtalbot · 2023-09-11T16:44:05Z

Changes:

Changed order to start with motivation then become more specific
Try to introduce the topic of the cache before describing how to use it.
Add an additional catch for missing directories within --vep_cache and --snpeff_cache.

PR checklist

Changes: - Changed order to start with motivation then become more specific - Try to introduce the topic of the cache before describing how to use it.

github-actions · 2023-09-11T16:46:18Z

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

Posted for pipeline commit a236eab

+| ✅ 140 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   4 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: .github/workflows/awsfulltest.yml
nextflow_config - Config manifest.version should end in dev: 3.3.0
schema_lint - Input mimetype is missing or empty
schema_description - No description provided in schema for parameter: input_restart

❔ Tests ignored:

files_exist - File is ignored: conf/modules.config
files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
actions_ci - actions_ci
template_strings - template_strings
schema_params - schema_params
multiqc_config - multiqc_config

✅ 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: 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-sarek_logo_light.png
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-sarek_logo_light.png
files_exist - File found: docs/images/nf-core-sarek_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: lib/nfcore_external_java_deps.jar
files_exist - File found: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
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: lib/WorkflowSarek.groovy
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: .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-sarek_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: .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
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 - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.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
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.9
Run at 2023-09-12 15:41:31

docs/usage.md

maxulysse · 2023-09-11T17:39:50Z

Can you update CHANGELOG

docs/usage.md

FriederikeHanssen

Awesome ❤️ every time I read it it gets more and more clear. Some small suggestions when reading through it, but looks great already

docs/usage.md

Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

…k into cache_docs_improvements

docs/usage.md

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

docs/usage.md

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

Update documentation around VEP and snpEff cache

dcb3268

Changes: - Changed order to start with motivation then become more specific - Try to introduce the topic of the cache before describing how to use it.

adamrtalbot requested a review from maxulysse as a code owner September 11, 2023 16:44

adamrtalbot added 4 commits September 11, 2023 17:55

Add catch for VEP and snpeff cache to make sure they exist

154be9b

Improved error message

ad61ed0

fix snpEff capitalisation

5ea3167

Add tests to check if cache exists prior to running

d702438

maxulysse reviewed Sep 11, 2023

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maxulysse and others added 7 commits September 12, 2023 16:14

Merge branch 'dev' into cache_docs_improvements

88f795a

update CHANGELOG

213c878

Apply suggestions from code review

33de708

Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

polish

adc4352

merge stuff

f9938f4

update

851c5a6

Merge branch 'cache_docs_improvements' of github.com:adamrtalbot/sare…

c8536d8

…k into cache_docs_improvements

adamrtalbot commented Sep 12, 2023

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maxulysse added 2 commits September 12, 2023 17:21

polish

45fcca4

update

c30557c

adamrtalbot commented Sep 12, 2023

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Apply suggestions from code review

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Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

adamrtalbot commented Sep 12, 2023

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maxulysse approved these changes Sep 12, 2023

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Update docs/usage.md

a236eab

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

adamrtalbot merged commit 767e4af into nf-core:dev Sep 12, 2023

adamrtalbot deleted the cache_docs_improvements branch September 12, 2023 16:31

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Update documentation around VEP and snpEff cache#1222

Update documentation around VEP and snpEff cache#1222
adamrtalbot merged 16 commits intonf-core:devfrom
adamrtalbot:cache_docs_improvements

adamrtalbot commented Sep 11, 2023 •

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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maxulysse commented Sep 11, 2023

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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maxulysse commented Sep 11, 2023

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adamrtalbot commented Sep 11, 2023 •

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