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filter empty files #354

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merged 6 commits into from Nov 26, 2021
Merged

filter empty files #354

merged 6 commits into from Nov 26, 2021

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d4straub
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@d4straub d4straub commented Nov 25, 2021 •
edited

Closes #340

Sample with input files and files after cutadapt with low read numbers (gz'ed file size < 1Kb) are removed. Either with error that stops the pipeline or it continues when using --ignore_empty_input_files or --ignore_failed_trimming. Either way, an error message with sample names will highlight what samples were failing.

I did not add a check after DADA2's quality filter filtntrim, because the error message there is actually quite clear.

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).
  • 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 Nov 25, 2021 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6b2e477

+| ✅ 136 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.

✅ Tests passed:

Run details

  • nf-core/tools version 2.1
  • Run at 2021-11-26 10:31:13

erikrikarddaniel
erikrikarddaniel approved these changes Nov 26, 2021
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Fine.

@d4straub
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d4straub commented Nov 26, 2021 •
edited

Thanks Daniel!

I thought I have have solved all issues, but now the RDP database that we use for tests was not accessible, all tests fail cause of
Can't stage file https://zenodo.org/record/4310151/files/rdp_species_assignment_18.fa.gz -- reason: Connection refused (Connection refused). I'll restart tests.

Edit: Still cannot download the taxonomy files, I'll wait and will re-start tests later.
Edit2: Now it succeeded!

@d4straub d4straub merged commit b10adc1 into nf-core:dev Nov 26, 2021
@d4straub d4straub deleted the filter-empty-files branch November 26, 2021 13:10
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