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Issue 950: samplesheet validation - no spaces in sample or patient names #978

Merged
merged 3 commits into from
Mar 28, 2023
Merged

Issue 950: samplesheet validation - no spaces in sample or patient names #978

merged 3 commits into from
Mar 28, 2023

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matrulda
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@matrulda matrulda commented Mar 28, 2023 •
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This fixes #950

Note that the pipeline is terminated using System.exit() which isn't recommended (nf-core/tools#1840). But I leave that for another PR since it has to be changed in multiple places.

Tested successfully (locally) with:

TMPDIR=~ PROFILE=docker pytest --tag sample_with_space  --symlink --kwdof --git-aware --color=yes

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/sarek 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).

@matrulda matrulda changed the title Issue 950 samplesheet validation no spaces Issue 950: samplesheet validation - no spaces in sample or patient names Mar 28, 2023
@matrulda matrulda marked this pull request as draft March 28, 2023 09:16
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github-actions bot commented Mar 28, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit d48cc24

+| ✅ 152 tests passed       |+
#| ❔   8 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-03-28 11:28:41

@matrulda matrulda force-pushed the issue-950_samplesheet_validation_no_spaces branch from a579ed2 to 3e52960 Compare March 28, 2023 10:54
@matrulda matrulda force-pushed the issue-950_samplesheet_validation_no_spaces branch from 3e52960 to 8227588 Compare March 28, 2023 11:01
@matrulda matrulda marked this pull request as ready for review March 28, 2023 11:05
@maxulysse
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maxulysse commented Mar 28, 2023 •
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Can you add this bit in tests/config/tags.yml? (EDIT: before L53)

validation_checks:
  - conf/modules/**
  - main.nf
  - modules/**
  - nextflow.config
  - nextflow_schema.json
  - subworkflows/**
  - tests/test_skip_markduplicates.yml
  - workflows/**

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And also this part in .github/workflows/pytest-workflow.yml in the exclude part (around L41-L57)

          - profile: "singularity"
            tags: validation_checks
          - profile: "conda"
            tags: validation_checks

@matrulda
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Thanks @maxulysse ! I think I fixed it all now :)

@matrulda matrulda merged commit ee7656f into nf-core:dev Mar 28, 2023
@matrulda matrulda mentioned this pull request Mar 29, 2023
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