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Implement chunking to speed up alignment #105

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Implement chunking to speed up alignment #105

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reichan1998
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Fixes #35 and #74

  • Add module SEQKIT_SPLIT2 to split FASTQ input
  • Add module SAMTOOLS_SPLIT to split CRAM input

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
Implement chunking to speed up alignment:
ff3f350 
- Add `SEQKIT_SPLIT2` to split FASTQ file for `align_short`, `align_pacbio` and `align_ont`
- Add `SAMTOOLS_SPLIT` to split CRAM/BAM file for `align_short` if input type contains CRAM
@reichan1998
Add seqkit/split2
044eef2
@reichan1998
edit align_short.nf
10d91fd
@reichan1998 reichan1998 requested a review from tkchafin August 13, 2024 10:23
@reichan1998 reichan1998 deleted the implement_chunking branch September 17, 2024 04:26
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@reichan1998