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Trim by lib #807

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Merged
jfy133 merged 9 commits into from
Nov 24, 2021
Merged

Trim by lib #807

jfy133 merged 9 commits into from
Nov 24, 2021

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@TCLamnidis
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@TCLamnidis TCLamnidis commented Nov 18, 2021 •
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Closes #805

This PR changes the behaviour of the bam_trim process, to allow separate trimming parameters not only by UDG treatment but also by library strandedness. This can be important for creating broader stable profiles that deal with complex datasets in a more transparent way.
Also corrected the stated default value for bam trimming in the parameter helptext. The helptext stated 1 bp would be trimmed on each end, but the actual default was 0.

Added Parameters:
bamutils_clip_double_stranded_half_udg_left
bamutils_clip_double_stranded_half_udg_right
bamutils_clip_double_stranded_none_udg_left
bamutils_clip_double_stranded_none_udg_right
bamutils_clip_single_stranded_half_udg_left
bamutils_clip_single_stranded_half_udg_right
bamutils_clip_single_stranded_none_udg_left
bamutils_clip_single_stranded_none_udg_right

Removed Parameters:
bamutils_clip_half_udg_left
bamutils_clip_half_udg_right
bamutils_clip_none_udg_left
bamutils_clip_none_udg_right

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • 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 Nov 18, 2021

Markdown linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install markdownlint-cli
  • Fix the markdown errors
    • Automatically: markdownlint . --config .github/markdownlint.yml --fix
    • Manually resolve anything left from markdownlint . --config .github/markdownlint.yml

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

@TCLamnidis TCLamnidis requested a review from jfy133 November 18, 2021 10:30
jfy133
jfy133 approved these changes Nov 18, 2021
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LGTM

@jfy133 jfy133 merged commit b2e2256 into dev Nov 24, 2021
@TCLamnidis TCLamnidis deleted the trim_by_lib branch January 12, 2022 15:59
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@TCLamnidis @jfy133