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Make ancient DNA damage correction optional #459

Merged
merged 6 commits into from
Jun 22, 2023
Merged

Make ancient DNA damage correction optional #459

merged 6 commits into from
Jun 22, 2023

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jfy133
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@jfy133 jfy133 commented Jun 16, 2023 •
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This makes the damage correction subworkflow optional, i.e. ytou can run just pyDamage, and optionally turn on damage correction using freebayes and bcftools.

@alexhbnr please can you test, and let me know if you would refer to have it opt in (rather than opt out).

Also note this does not yet include the hotfix in the patch for #449 , I will add that later as it requires more thinking due to the more complex inputs to bin refinement since domain classification has come in.

fixes #456

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/mag branch on the nf-core/test-datasets repository.
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  • Output Documentation in docs/output.md is updated.
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@jfy133 jfy133 changed the base branch from master to dev June 16, 2023 16:21
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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @jfy133,

It looks like this pull-request is has been made against the jfy133/nf-core-mag master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the jfy133/nf-core-mag dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

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github-actions bot commented Jun 16, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9143958

+| ✅ 158 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-06-21 06:56:57

@jfy133 jfy133 linked an issue Jun 16, 2023 that may be closed by this pull request
Split ancientDNA sub-workflow into separate sub-workflows for running damage analysis and consensus correction #456
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@jfy133 jfy133 requested review from maxibor and alexhbnr June 16, 2023 16:25
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jfy133 commented Jun 16, 2023
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The skipping of the contig correction itself works well. However, when activating --skip_ancient_damagecorrection pyDamage doesn't export the files into a sample specific sub-folder any longer. The usual way was that pyDamage has sample-specific sub-folders in Ancient_DNA/pydamage/analyze and Ancient_DNA/pydamage/filter. At the moment, for every sample the same file is used and the results of the previous run sample are overwritten.

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jfy133 commented Jun 21, 2023
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jfy133 commented Jun 21, 2023

Fix applied, waiting from results on tests as discussed on slack.

@jfy133 jfy133 requested a review from alexhbnr June 21, 2023 08:06
@jfy133 jfy133 merged commit 92c69e6 into nf-core:dev Jun 22, 2023
@jfy133 jfy133 deleted the split-adna-workflow branch June 28, 2023 13:25
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@alexhbnr alexhbnr alexhbnr approved these changes

@maxibor maxibor Awaiting requested review from maxibor

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Split ancientDNA sub-workflow into separate sub-workflows for running damage analysis and consensus correction
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