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Fix pipeline not running without --vep_cache #553

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merged 12 commits into from
Feb 17, 2025
Merged

Fix pipeline not running without --vep_cache #553

merged 12 commits into from
Feb 17, 2025

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fellen31
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@fellen31 fellen31 commented Feb 10, 2025 •
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Closes #547. Should also close #519, since the pipeline now looks for all workflows required by a file, not just the first.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Feb 10, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8447146

+| ✅ 185 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

❔ Tests ignored:

  • files_exist - File is ignored: CITATIONS.md
  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-nallo_logo_light.png
  • files_exist - File is ignored: docs/README.md
  • files_exist - File is ignored: docs/images/nf-core-nallo_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-nallo_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-nallo_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nallo_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nallo_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2025-02-17 10:16:49

@fellen31 fellen31 changed the title Patch Fix pipeline not running without --vep_cache Feb 10, 2025
fellen31
fellen31 commented Feb 10, 2025
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@fellen31 fellen31 linked an issue Feb 10, 2025 that may be closed by this pull request
Not able to run nallo without --vep_cache #547
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@fellen31 fellen31 marked this pull request as ready for review February 10, 2025 12:33
@fellen31 fellen31 requested a review from a team as a code owner February 10, 2025 12:33
@fellen31 fellen31 mentioned this pull request Feb 10, 2025
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@fellen31 fellen31 linked an issue Feb 10, 2025 that may be closed by this pull request
GENOMICMEDICINESWEDEN_NALLO:NALLO:SHORT_VARIANT_CALLING:DEEPVARIANT 'Path value cannot be null' #519
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rannick
rannick approved these changes Feb 11, 2025
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LGTM

fellen31
fellen31 commented Feb 17, 2025
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Two tests are failing, this is due to being run with the master code (pull_request_target). Since this PR contains the fix, the pull_request_target test will always fail. The tests run successfully with the branch code (pull_request). I've removed the pull_request_target from the GitHub workflow in the latest commit: 8447146, so that this will not be an issue in the future.

@fellen31 fellen31 merged commit 138f006 into master Feb 17, 2025
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@fellen31 fellen31 mentioned this pull request Feb 18, 2025
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fellen31 added a commit that referenced this pull request Feb 27, 2025
@fellen31
Merge master into dev (#576)
d5cf0c1 
* Fix pipeline not running without `--vep_cache` (#553)

* Fix pipeline can't run without

* CHANGELOG

* docs

* docs

* update snaps

* fix CI

* Update CHANGELOG.md

* changelog date

* Add vep_plugin_files to files check

* CHANGELOG

* Update CHANGELOG.md

* always failing CI because of nf-core update

* CHANGELOG
fellen31 added a commit that referenced this pull request Mar 3, 2025
@fellen31 @padraicc
@jemten @rannick
Release 0.5.0 (#581)
74ff9f3 
* bump version (#530)

* Add credits (#531)

* Add missing credits

* update changelog

* Assemble ONT genomes (#516)

* Assemble ONT genomes

* hifiasm 0.24.0

* update tests

* update patch

* Template update for nf-core/tools version 3.1.1 (#532)

* Initial template commit

* Template update for nf-core/tools version 3.1.2.dev0

* Template update for nf-core/tools version 3.1.1

* changelog

* merge mistake

* merge mistake

* merge mistake

* merge mistakes

* fix lint

* update ci

* fix version

* fix tests

* fix RO crate

* remove nf-core reference

* bump deepvariant version (#535)

* Output per-base depth in d4 format (#537)

* output per-base depth in d4 format

* Changelog

* update nf-core module

* Downgrade to Sniffles1 (#536)

* Downgrade to Sniffles1

* Update CHANGELOG.md

* bump deepvariant version (#535)

* fix readme

* Add skip for SV calling

* Template sync 3.1.2 (#541)

* Initial template commit

* Template update for nf-core/tools version 3.1.2.dev0

* Template update for nf-core/tools version 3.1.2.dev0

* Template update for nf-core/tools version 3.1.2.dev0

* Template update for nf-core/tools version 3.1.1

* Template update for nf-core/tools version 3.1.1

* use ro-crate command

* changelog

* update workflow dependencies

* make sv filtering conditional on skip_sv_calling param

* style: fix text alignment

* style: fix linting issue

* update changelog

* fix linting issues in CHANGELOG.md param table

* Run CI tests with latest-stable version of Nextflow (#545)

* Run CI tests with latest-stable version of nextflow

* Changelog

* Fix naming mistakes in output docs (#546)

* Fix naming mistakes in output docs

* Changelog and prettier

* Update docs/output.md

Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>

* prettier

---------

Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>

* change vcf headers, merge by sample, merge by case, first draft for merging paraphase json

* add script to merge json files

* update changelog

* fixes

* add arg for bcftools query

* add prefix to CREATE_SAMPLES_FILE

* use arg2

* modify create_sample_files to add the haplotype in the sample name

* haplotype specific sample names, force single

* Fix naming for SNVs and pipeline not running with (#556)

* create empty channels to use

* update paraphase

* updated snapshots

* update snapshots

* Update CHANGELOG.md

Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>

* Update modules/local/merge_json.nf

Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>

* Update modules/local/merge_json.nf

Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>

* Update conf/modules/call_paralogs.config

Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>

* Update conf/modules/call_paralogs.config

Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>

* Update modules/local/merge_json.nf

Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>

* Apply suggestions from code review

Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>

* case to family and aligned bracket

* multi-argument formatting

* use groupTuple

* add merge json

* add executing permissions to script

* update script

* update script

* update script

* add to software references

* fix config issue

* remove snapshots

* update snaphshots

* exclude vcf and tbi unpublished

* update snaps

* remove snap

* add publish dir

* update snap

* revert change

* paralogs false default publish, remove publishing for all but family merged vcf

* use family_id directory

* prettier

* updated modules added

* update output.md

* publish family json

* update snapshots

* use sample and family directories, update mapping for family merging

* update snapshots

* Update docs/output.md

Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>

* prettier

* Limit VEP to 1 cpu while bugged (#558)

* Bump Severus to 1.3 (#557)

* Bump Severus version

* Update CHANGELOG.md

* Always run all SV callers (#542)

* Downgrade to Sniffles1

* Update CHANGELOG.md

* bump deepvariant version (#535)

* Always run multiple SV-callers

* changelog

* changelog

* update tests and ci

* Also output CNV-calls

* CHANGELOG

* update conf

* wip

* update docs+tests

* remove rouge versions.yml

* Template update to v3.2.0 (#560)

* Initial template commit

* Template update for nf-core/tools version 3.1.2.dev0

* Template update for nf-core/tools version 3.1.1

* Template update for nf-core/tools version None

* Template update for nf-core/tools version None

* CHANGELOG

* Patch to dev (#565)

* Fix pipeline can't run without

* CHANGELOG

* docs

* docs

* update snaps

* fix CI

* Update CHANGELOG.md

* changelog date

* Add vep_plugin_files to files check

* CHANGELOG

* Update CHANGELOG.md

* always failing CI because of nf-core update

* Replace dipcall (#566)

* wip

* Replace dipcall

* Replace dipcall

* description

* Update CHANGELOG

* ignore bam md5

* CHANGELOG

* Update main.nf

* Update workflows/nallo.nf

Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>

---------

Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>

* Fix filter SNVs tries to run even with --skip_snv_calling (#570)

* Fix filter SNVs tries to run even with --skip_snv_calling

* CHANGELOG

* Update CHANGELOG.md

* Fix unsorted sniffles1 variants (#572)

* Fix unsorted sniffles1 variants

* update tests

* Update metro map (#573)

* CHANGELOG

* Add contributors to `nextflow.config` (#574)

* Add contributors to config

* Add missing

* Fix a few language server issues (#533)

* start fixing language server issues

* revert some changes, remove encode

* fix some more

* Update main.nf

* update methylation tests

* Fix nextflow.config issues (#578)

* Fix sniffles1 (#580)

* Fix sniffles1

* fix lint

* Add missing nf-test triggers

* update snaps

* remove missed dipcall references (#577)

* Merge master into dev (#576)

* Fix pipeline not running without `--vep_cache` (#553)

* Fix pipeline can't run without

* CHANGELOG

* docs

* docs

* update snaps

* fix CI

* Update CHANGELOG.md

* changelog date

* Add vep_plugin_files to files check

* CHANGELOG

* Update CHANGELOG.md

* always failing CI because of nf-core update

* CHANGELOG

* Update CHANGELOG.md

* Fix project samplesheet validation (#584)

* Fix mistake in usage docs (#586)

* Update usage.md

* changelog

* Prep release 0.5.0 (#585)

* Bump version 0.5.0

* CHANGELOG

* update snaps

* Review comments (#589)

---------

Co-authored-by: padraicc <padraic.corcoran@scilifelab.uu.se>
Co-authored-by: Pádraic Corcoran <padraicc@users.noreply.github.com>
Co-authored-by: padraicc <padraic.corcoran£scilifelab.uu.se>
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
Co-authored-by: Annick Renevey <47788523+rannick@users.noreply.github.com>
Co-authored-by: Annick Renevey <annick.renevey@scilifelab.se>
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