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Patch release v1.1.1 #388

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Merged
merged 5 commits into from
Jul 26, 2023
Merged

Patch release v1.1.1 #388

merged 5 commits into from
Jul 26, 2023

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@ramprasadn
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@ramprasadn ramprasadn commented Jul 25, 2023 •
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Description

  • Configures bcftools merge to generate compressed vcf files.
  • Fixes errors thrown by bcftools concat due to sample names in input vcf files not being in same order.
    • GATK's MergeVcfs can handle such differences hence, the switch. However, GATK complains about spaces in the INFO columns so I have added a small groovy function to create a reformatted vcf file.

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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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 Jul 25, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5c89cd1

+| ✅ 153 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.1.1
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-26 08:39:40

@ramprasadn ramprasadn marked this pull request as ready for review July 25, 2023 16:50
asp8200
asp8200 reviewed Jul 26, 2023
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asp8200
asp8200 reviewed Jul 26, 2023
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asp8200
asp8200 approved these changes Jul 26, 2023
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LGTM

jfy133
jfy133 approved these changes Jul 26, 2023
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CHANGELOG.md Outdated
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## v1.1.1 - Abu (Patch) [xxxx-xx-xx]
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@jfy133 jfy133 Jul 26, 2023

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Set date!

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@ramprasadn ramprasadn Jul 26, 2023 •
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Done! 😄

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ramprasadn commented Jul 26, 2023

Thanks for the review @asp8200 and @jfy133 👍🏻

@ramprasadn ramprasadn merged commit c371602 into nf-core:master Jul 26, 2023
@ramprasadn ramprasadn deleted the patch branch August 1, 2023 14:15
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@ramprasadn @jfy133 @asp8200