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feat added MT deletion script #349

Merged
merged 17 commits into from
May 30, 2023
Merged

feat added MT deletion script #349

merged 17 commits into from
May 30, 2023

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Lucpen
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@Lucpen Lucpen commented May 23, 2023 •
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PR checklist

  • Added Daniels script for MT deletion detection as is used in MIP
  • 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).

@Lucpen Lucpen marked this pull request as draft May 23, 2023 13:55
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Lucpen commented May 23, 2023

The script runs only on the non-shifted MT bam. It think it would be an overkill to run it on both or merging the shifted and unshifted bam just to run it.

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github-actions bot commented May 23, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 203d9f8

+| ✅ 154 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '1.0.0'
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 2023-05-30 12:11:09

@Lucpen Lucpen marked this pull request as ready for review May 23, 2023 14:25
@Lucpen Lucpen requested a review from jemten May 23, 2023 14:25
@Lucpen Lucpen added enhancement Improvement for existing functionality ready for review PR is ready for review labels May 23, 2023
jemten
jemten reviewed May 24, 2023
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Nice! Could you add a line to the readme and output documentation

modules/local/mt_deletion_scritp.nf Outdated Show resolved Hide resolved
subworkflows/local/mitochondria/align_and_call_MT.nf Outdated Show resolved Hide resolved
modules/local/mt_deletion_scritp.nf Outdated Show resolved Hide resolved
jemten
jemten reviewed May 25, 2023
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Some small typos :)

modules/local/mt_deletion_scritp.nf Outdated Show resolved Hide resolved
modules/local/mt_deletion_scritp.nf Outdated Show resolved Hide resolved
subworkflows/local/mitochondria/align_and_call_MT.nf Outdated Show resolved Hide resolved
subworkflows/local/mitochondria/align_and_call_MT.nf Outdated Show resolved Hide resolved
Lucpen and others added 4 commits May 25, 2023 15:57
@Lucpen @jemten
Update modules/local/mt_deletion_scritp.nf
2365678 
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
@Lucpen @jemten
Update subworkflows/local/mitochondria/align_and_call_MT.nf
7162cd7 
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
@Lucpen @jemten
Update subworkflows/local/mitochondria/align_and_call_MT.nf
a9a9554 
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
fix renamed local module
ed6b2f5
jemten
jemten reviewed May 29, 2023
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Nice! Only one small comment on the publish directory and could you update the changelog as well.

conf/modules/align_and_call_MT.config Show resolved Hide resolved
lucia.pena.perez@scilifelab.se added 2 commits May 30, 2023 12:10
@Lucpen Lucpen merged commit b9bac75 into devplaceholder May 30, 2023
@Lucpen Lucpen deleted the add_deletion_script branch May 30, 2023 12:26
@Lucpen Lucpen mentioned this pull request Jun 1, 2023
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@jemten jemten jemten approved these changes

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