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Added contig tag to vcf in ivar_variants_to_vcf and included bcftools sort for vcf sorting #308

Merged
merged 14 commits into from
Jul 7, 2022
Merged

Added contig tag to vcf in ivar_variants_to_vcf and included bcftools sort for vcf sorting #308

merged 14 commits into from
Jul 7, 2022

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saramonzon
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@saramonzon saramonzon commented Apr 26, 2022 •
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Added reference parameter for including a contig tag in vcf file for ivar_variants_to_vcf script. Thanks to this tag now vcf sorting can be directly done using bcftools sort module.

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
    • 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 Apr 26, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 02a8487

+| ✅ 139 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: lib/WorkflowViralrecon.groovy
  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-06-04 16:40:18

@heuermh
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heuermh commented May 2, 2022

Curious why one check is reported here as not completed yet but the action run summary here looks ok

https://github.com/nf-core/viralrecon/actions/runs/2225674949

drpatelh
drpatelh reviewed Jul 7, 2022
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drpatelh
drpatelh reviewed Jul 7, 2022
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Thanks @saramonzon ! Just some aesthetic changes required.

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drpatelh commented Jul 7, 2022

Don't worry. I will fix these in an upcoming PR.

@drpatelh drpatelh merged commit 9d193d0 into nf-core:dev Jul 7, 2022
drpatelh added a commit to drpatelh/nf-core-viralrecon that referenced this pull request Jul 7, 2022
@drpatelh
Follow up fix for PR nf-core#308
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@drpatelh drpatelh mentioned this pull request Jul 8, 2022
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@heuermh heuermh heuermh approved these changes

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@saramonzon @heuermh @drpatelh