Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

fix vcf_collect when a tool is absent #458

Merged
merged 4 commits into from Jan 31, 2024
Merged

fix vcf_collect when a tool is absent #458

merged 4 commits into from Jan 31, 2024

Conversation

rannick
Copy link
Collaborator

@rannick rannick commented Dec 20, 2023 •
edited

Fixing bug.
Behavior with bug:
VCF_COLLECT failing when one or more of fusioncatcher, arriba or starfusion was not used.

Behavior with fix:
VCF_COLLECT (and the whole pipeline) completes taking into account any tool given.

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! Te
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/rnafusion branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile 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).

@github-actions GitHub Actions
Copy link

github-actions bot commented Dec 20, 2023 •
edited

nf-core lint overall result: Failed ❌

Posted for pipeline commit 887624c

+| ✅ 159 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!
-| ❌  11 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/nfcore_external_java_deps.jar
  • nextflow_config - Config default value incorrect: params.ensembl_version is set as 105 in nextflow_schema.json but is 102 in nextflow.config.
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - assets/email_template.html does not match the template
  • files_unchanged - assets/email_template.txt does not match the template
  • files_unchanged - assets/nf-core-rnafusion_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-rnafusion_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-rnafusion_logo_dark.png does not match the template
  • files_unchanged - pyproject.toml does not match the template

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • pipeline_todos - TODO string in WorkflowRnafusion.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12
  • Run at 2024-01-31 09:34:33

@rannick rannick self-assigned this Jan 29, 2024
@rannick
Copy link
Collaborator Author

rannick commented Jan 31, 2024

Tested with success:

[a1/27673f] Submitted process > NFCORE_RNAFUSION:RNAFUSION:INPUT_CHECK:SAMPLESHEET_CHECK (tendergoose_samplesheet.csv)
[4c/eb9b44] Submitted process > NFCORE_RNAFUSION:RNAFUSION:TRIM_WORKFLOW:FASTP (tendergoose)
[68/860ae4] Submitted process > NFCORE_RNAFUSION:RNAFUSION:FASTQC (tendergoose)
[b1/931501] Submitted process > NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:STAR_FOR_ARRIBA (tendergoose)
[c4/2ce606] Submitted process > NFCORE_RNAFUSION:RNAFUSION:TRIM_WORKFLOW:FASTQC_FOR_FASTP (tendergoose)
[7d/087e92] Submitted process > NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:SAMTOOLS_SORT_FOR_ARRIBA (tendergoose)
[cf/e40558] Submitted process > NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:ARRIBA (tendergoose)
[e8/195aa4] Submitted process > NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:SAMTOOLS_VIEW_FOR_ARRIBA (tendergoose)
[2a/0d333a] Submitted process > NFCORE_RNAFUSION:RNAFUSION:FUSIONREPORT_WORKFLOW:FUSIONREPORT (tendergoose)
[70/6cbd28] Submitted process > NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:SAMTOOLS_INDEX_FOR_ARRIBA (tendergoose)
[11/c55bc7] Submitted process > NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (tendergoose)
[e0/3bf080] Submitted process > NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (tendergoose)
[17/9578f0] Submitted process > NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:VCF_COLLECT (tendergoose)
[b6/001b19] Submitted process > NFCORE_RNAFUSION:RNAFUSION:CUSTOM_DUMPSOFTWAREVERSIONS (1)
[8a/2d1544] Submitted process > NFCORE_RNAFUSION:RNAFUSION:MULTIQC
-[nf-core/rnafusion] Pipeline completed successfully-
-[nf-core/rnafusion] Pipeline completed successfully-

@rannick rannick marked this pull request as ready for review January 31, 2024 09:34
@rannick rannick requested a review from fevac January 31, 2024 09:35
@rannick
Copy link
Collaborator Author

rannick commented Jan 31, 2024

Linting issues come from nf-tools update to 2.12

fevac
fevac approved these changes Jan 31, 2024
View reviewed changes
Copy link
Contributor

@fevac fevac left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks good! A bit confusing with the changelog but otherwise looks good 🌟

@rannick rannick merged commit ffe9c09 into dev Jan 31, 2024
7 of 8 checks passed
@rannick rannick deleted the absent_tools branch January 31, 2024 10:28
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@fevac fevac fevac approved these changes

Assignees

@rannick rannick

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
2 participants
@rannick @fevac