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Filter by assemblies length #11

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5 tasks
davidtong28 opened this issue Jul 6, 2023 · 0 comments
Open
5 tasks

Filter by assemblies length #11

davidtong28 opened this issue Jul 6, 2023 · 0 comments
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@azmigueldario
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enhancement New feature or request

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@davidtong28
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davidtong28 commented Jul 6, 2023 •
edited by azmigueldario
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Description of feature

Add a skippable step in post assembly QC to filter out unwanted assembly length. The length may come from the Quast report. This is most useful in WGS of a known species. Parameters should include:

  • Add skip_length_filter=True
  • Add param for min_length
  • (Optional) add max_length
  • Install seqkit_seq module from nf-core
  • Integrate into a subworkflow
@davidtong28 davidtong28 added the enhancement New feature or request label Jul 6, 2023
@aimirza aimirza self-assigned this Nov 7, 2023
aimirza added a commit that referenced this issue Dec 19, 2023
@aimirza
added seqtk/subseq module for issue #11
69d1588
@aimirza aimirza removed their assignment Nov 27, 2024
@azmigueldario azmigueldario self-assigned this Dec 9, 2024
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refs/heads/11-filter-by-assemblies-length cidgoh/bacpaq
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@aimirza @davidtong28 @azmigueldario