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Fix filters with --input_fasta #630

Merged
merged 9 commits into from
Aug 31, 2023
Merged

Fix filters with --input_fasta #630

merged 9 commits into from
Aug 31, 2023

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d4straub
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@d4straub d4straub commented Aug 30, 2023 •
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Closes #629

Also added verbose error message if ASV length or codon filter remove all ASVs. rRNA filter had such an error already.

Fixed:

nextflow run ampliseq -profile test_fasta,singularity --outdir results_fasta -resume --max_len_asv 265
nextflow run ampliseq -profile test_fasta,singularity --outdir results_fasta -resume --filter_ssu bac
nextflow run ampliseq -profile test_fasta,singularity --outdir results_fasta -resume --filter_codons --orf_end 3
nextflow run ampliseq -profile test_fasta,singularity --outdir results_fasta -resume --filter_codons --orf_end 30 --max_len_asv 265 --filter_ssu bac

Will not fix:
nextflow run ampliseq -profile test_fasta,singularity --outdir results_fasta -resume --vsearch_cluster
therefore no VSEARCH clustering will be available with fasta file input. If need be that can be fixed in another PR.

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
  • If necessary, also make a PR on the nf-core/ampliseq 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 --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).

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github-actions bot commented Aug 30, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 928beeb

+| ✅ 152 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-31 11:06:55

erikrikarddaniel
erikrikarddaniel approved these changes Aug 30, 2023
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👍

Is a change log entry warranted -- this report is completely new, right, so I suppose no?

@d4straub
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Thanks for the approval but I attempt to fix test_fasta with all functionality, so I will add a few more commits ;)

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I had two minutes before a meeting... ;-)

@d4straub d4straub changed the title fix --max_len_asv Fix filters with --input_fasta Aug 31, 2023
@d4straub d4straub marked this pull request as ready for review August 31, 2023 12:03
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Alright, I think all is fine.

@d4straub d4straub merged commit 3836612 into nf-core:dev Aug 31, 2023
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@d4straub d4straub deleted the fix-test_fasta branch August 31, 2023 12:44
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@d4straub @erikrikarddaniel