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Added UCSC BedgraphtoBigwig and NCRNA crosslink publish fix #139

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Added UCSC BedgraphtoBigwig and NCRNA crosslink publish fix #139

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Chromojones
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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).

@Chromojones
adding new module bedgraphtobigwig
022e39f
@Chromojones
added line 6-8 imports to resolve_groupings_and_crosslinks.nf, added …
1e99524 
…line 16 ch_chrom_sizes, added modules bigwiggenome individual, individual_withgroup, group_withgroup, updated modules.config to include bigwiggenome and fix ncrna input to publish ncrna crosslinks
@Chromojones Chromojones reopened this Mar 24, 2025
@CharlotteAnne
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NOTE: need to amend this PR to produce separate bigwigs for +ve and -ve strand of bedgraph

@CharlotteAnne CharlotteAnne linked an issue Mar 26, 2025 that may be closed by this pull request
add ucsc bedgraph->bigwig to pipeline as BSF input #126
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add ucsc bedgraph->bigwig to pipeline as BSF input
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@Chromojones @CharlotteAnne