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added skip_bowtie parameter to make bowtie alignment optional #155

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added skip_bowtie parameter to make bowtie alignment optional #155

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@karenirawan karenirawan commented Mar 25, 2025 •
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Added skip_bowtie parameter that skips bowtie index creation, bowtie alignment, and enables icount summary

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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/clipseq 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).
  • 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).

@karenirawan
rna_align.nf - added line 36 skip_bowtie input as Boolean\defined unm…
742dc95 
…apped fastq as input fastq line 45define empty channel premapping log line 46

added if skip_bowtie , changed input for star align to unmapped fastq
added skip_bowtie to nextflow.config = false
added skip_bowtie param to clipseq workflow
@karenirawan
skip bowtie index creation, skip bowtie alignment, enable icount_summ…
310ec7e 
…ary IF bowtie alignment skipped
@karenirawan karenirawan changed the base branch from master to feat-2-0 March 25, 2025 16:49
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github-actions bot commented Mar 25, 2025

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 @karenirawan,

It looks like this pull-request is has been made against the karenirawan/clipseq 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 karenirawan/clipseq 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.

Thanks again for your contribution!

@CharlotteAnne CharlotteAnne linked an issue Mar 26, 2025 that may be closed by this pull request
Make bowtie pre-mapping optional #116
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Make bowtie pre-mapping optional

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@karenirawan @CharlotteAnne