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add chromograph #366

Merged
merged 6 commits into from
Jun 27, 2023
Merged

add chromograph #366

merged 6 commits into from
Jun 27, 2023

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ramprasadn
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@ramprasadn ramprasadn commented Jun 26, 2023 •
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PR checklist

This PR adds chromograph to visualize the output from upd module.

  • 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 Jun 26, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3467911

+| ✅ 156 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • 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 2.8
  • Run at 2023-06-26 17:35:09

@ramprasadn ramprasadn changed the title add chromograph [skip ci] add chromograph Jun 26, 2023
@ramprasadn ramprasadn marked this pull request as ready for review June 26, 2023 16:47
@ramprasadn ramprasadn requested review from jemten and Lucpen June 26, 2023 17:47
Lucpen
Lucpen reviewed Jun 27, 2023
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CHANGELOG.md
Comment on lines +10 to +16
- Add `public_aws_ecr` profile for using AWS ECR public gallery images [#360](https://github.com/nf-core/raredisease/pull/360)
- GATK's ShiftFasta to generate all the files required for mitochondrial analysis [#354](https://github.com/nf-core/raredisease/pull/354)
- Feature to calculate CADD scores for indels [#325](https://github.com/nf-core/raredisease/pull/325)
- HmtNote to annotate mitochondria [#355](https://github.com/nf-core/raredisease/pull/355)
- MT del script to detect mitochondrial deletions [#349](https://github.com/nf-core/raredisease/pull/349)
- eKLIPse to identify large mitochondrial deletions [#365](https://github.com/nf-core/raredisease/pull/365)
- UPD+Chromograph to identify and visualize UPD sites and regions in the chromosomes [#364](https://github.com/nf-core/raredisease/pull/364) and [#366](https://github.com/nf-core/raredisease/pull/366)
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Thanks for adding the MT ones! :)

@ramprasadn ramprasadn merged commit a39e1d8 into nf-core:dev Jun 27, 2023
@ramprasadn ramprasadn deleted the chromograph branch June 27, 2023 07:30
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@Lucpen Lucpen Lucpen approved these changes

@jemten jemten Awaiting requested review from jemten

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@ramprasadn @Lucpen