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Change from file size to read counts as sample read threshold #597

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merged 4 commits into from Jun 19, 2023
Merged

Change from file size to read counts as sample read threshold #597

merged 4 commits into from Jun 19, 2023

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d4straub
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@d4straub d4straub commented Jun 15, 2023 •
edited

Closes #556

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 Jun 15, 2023 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 080d64a

+| ✅ 157 tests passed       |+
#| ❔   1 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 2.8
  • Run at 2023-06-19 11:18:59

tillenglert
tillenglert approved these changes Jun 19, 2023
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@tillenglert tillenglert left a comment

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Some minor comments, but looks good to me!

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nextflow_schema.json Outdated Show resolved Hide resolved
subworkflows/local/cutadapt_workflow.nf Outdated Show resolved Hide resolved
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subworkflows/local/parse_input.nf Outdated Show resolved Hide resolved
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d4straub and others added 2 commits June 19, 2023 13:15
@d4straub @tillenglert
Apply suggestions from code review
8ef7b73 
Co-authored-by: Till E. <64961761+tillenglert@users.noreply.github.com>
@d4straub
Update subworkflows/local/cutadapt_workflow.nf error message
080d64a
@d4straub d4straub merged commit 24596ee into nf-core:dev Jun 19, 2023
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@d4straub d4straub deleted the filtering-low-read-count-samples-in-qc branch June 19, 2023 12:21
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