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New ivar_variants_to_vcf.py #31

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New ivar_variants_to_vcf.py #31

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Shettland
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PR checklist

  • Refactored old ivar_variants_to_vcf.py with new functionalities like merging duplicate variants in the same position based on AF differencies and a new quality threshold.
  • 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- [ ] If necessary, also make a PR on the nf-core/viralrecon 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).

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github-actions bot commented May 14, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 693e554

+| ✅ 175 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   9 tests had warnings |!
-| ❌   7 tests failed       |-

❌ Test failures:

  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md 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
  • multiqc_config - assets/multiqc_config.yml not found.
  • base_config - conf/base.config contains withName:CUSTOM_DUMPSOFTWAREVERSIONS, but the corresponding process is not present in any of the Nextflow scripts.
  • modules_config - conf/modules.config contains withName:SAMPLESHEET_CHECK, but the corresponding process is not present in any of the Nextflow scripts.
  • modules_config - conf/modules.config contains withName:CUSTOM_DUMPSOFTWAREVERSIONS, but the corresponding process is not present in any of the Nextflow scripts.

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: conf/igenomes.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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
  • system_exit - System.exit in nanopore.nf: System.exit(1) [line 247]
  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-17 08:54:12

@github-actions GitHub Actions
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 43a22ad

+| ✅ 175 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   9 tests had warnings |!
-| ❌   7 tests failed       |-

❌ Test failures:

  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md 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
  • multiqc_config - assets/multiqc_config.yml not found.
  • base_config - conf/base.config contains withName:CUSTOM_DUMPSOFTWAREVERSIONS, but the corresponding process is not present in any of the Nextflow scripts.
  • modules_config - conf/modules.config contains withName:SAMPLESHEET_CHECK, but the corresponding process is not present in any of the Nextflow scripts.
  • modules_config - conf/modules.config contains withName:CUSTOM_DUMPSOFTWAREVERSIONS, but the corresponding process is not present in any of the Nextflow scripts.

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: conf/igenomes.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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
  • system_exit - System.exit in nanopore.nf: System.exit(1) [line 247]
  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-14 09:40:37

@Shettland Shettland closed this May 21, 2024
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@Shettland