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Presupplied ORFs functionality #264

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Presupplied ORFs functionality #264

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@jfy133 jfy133 commented Apr 26, 2023

Closes #255

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@jfy133 jfy133 marked this pull request as draft April 26, 2023 09:11
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github-actions bot commented Apr 26, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 258a49a

+| ✅ 159 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-05-31 13:16:38

@jfy133 jfy133 mentioned this pull request May 8, 2023
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jfy133 commented May 10, 2023

Status:

  1. samplesheet_check breaks if protein or feature is not phyiscally there, but should be OK if it's empty
  2. current issue if gff is missing
  3. if all columns filled, dump looks good for the input_check (need to now do a filter to send ORFs to skip annotation, and drop the channel elements for those not skipping annotation)

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Midnighter reviewed May 11, 2023
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These two changes should make the columns optional. Maybe you can add a comment making that clear.

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jfy133 commented May 31, 2023 •
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Done: synced with latest dev (With template)

To do:

  • Add to test datasets new samplesheet
  • Update test.configs
  • Test BGC workflow with and without supplied features files

To consider (separate PR):

  • Drop samplesheet check python entirely and switch to groovy valdiation; this would make row.protein and row.feature properly optional

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jfy133 commented Jul 12, 2023

Update: maybe make it possible to run just annotation (to get rid of that horrible if/else statement)?

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jfy133 commented Jul 19, 2023

Once #285 is merged, should sync with dev and replace the samplesheet input. This should make this much easier with input validation, which keeps breaking for some reason

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jfy133 commented Jul 26, 2023

I'm going to start from scratch as there are a lot of improvements that make this better

@jfy133 jfy133 closed this Nov 8, 2023
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