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Fix input schema to allow direct input again #537

Merged
merged 2 commits into from
Nov 7, 2023
Merged

Fix input schema to allow direct input again #537

merged 2 commits into from
Nov 7, 2023

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jfy133
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@jfy133 jfy133 commented Nov 7, 2023

Closes #536

Fixes the pattern and format type of the input validation to allow different types of files (i.e., both csv and fastq)

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/mag 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).

nvnieuwk
nvnieuwk approved these changes Nov 7, 2023
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LGTM :p I didn't know | could be used to define two patterns, that's a nice thing to know

mahesh-panchal
mahesh-panchal approved these changes Nov 7, 2023
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LGTM

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github-actions bot commented Nov 7, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f5d2dc2

+| ✅ 157 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowMag.groovy: Optionally add in-text citation tools to this list.
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-07 09:46:24

jfy133
jfy133 commented Nov 7, 2023
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jfy133 commented Nov 7, 2023

LGTM :p I didn't know | could be used to define two patterns, that's a nice thing to know

Seems to wor kanyway 👀

@jfy133 jfy133 merged commit f1cc2f3 into dev Nov 7, 2023
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@d4straub d4straub mentioned this pull request Nov 9, 2023
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@jfy133 jfy133 deleted the fix-input-schema branch January 22, 2024 07:46
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@nvnieuwk nvnieuwk nvnieuwk approved these changes

@mahesh-panchal mahesh-panchal mahesh-panchal approved these changes

@d4straub d4straub Awaiting requested review from d4straub

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@jfy133 @mahesh-panchal @nvnieuwk