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Include FASTA parameter, stage REF_CACHE and export REF_PATH #138

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Include FASTA parameter, stage REF_CACHE and export REF_PATH #138

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reichan1998
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Attempt to address issue #137

  • Enable the option to pass a FASTA file to SAMTOOLS_MERGE to avoid the lookup behaviour of samtools.
  • Generate the REF_PATH variable based on the original process outlined here using the seq_cache_populate.pl script.

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
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,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).

@reichan1998
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Hi @tkchafin, this approach is my proposal for handling CRAM files with samtools. It ensures that the reference FASTA is not retrieved multiple times and prevents errors when working with aligned CRAM inputs. Let me know if you'd like any further changes!

@reichan1998 reichan1998 requested a review from tkchafin October 24, 2024 09:39
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