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Upd fix #643

Merged
merged 4 commits into from
Nov 1, 2024
Merged

Upd fix #643

merged 4 commits into from
Nov 1, 2024

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jemten
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@jemten jemten commented Oct 30, 2024

PR checklist

Updated createCaseChannel function to include a check for maternal and paternal ids being set to a numeric 0.

Fix for #642

  • 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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

@jemten jemten linked an issue Oct 30, 2024 that may be closed by this pull request
Error in UPD on single sample #642
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github-actions bot commented Oct 30, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 86f0373

+| ✅ 200 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-30 16:13:59

@jemten jemten mentioned this pull request Oct 30, 2024
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@jemten jemten marked this pull request as ready for review October 31, 2024 07:49
fellen31
fellen31 reviewed Oct 31, 2024
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@fellen31 fellen31 left a comment

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Could the schema validation be changed instead to only allow a string or a 0?

E.g.

"paternal": {
                "oneOf": [
                    {
                        "type": "integer",
                        "enum": [0]
                    },
                    {
                        "type": "string",
                        "pattern": "^(\\S+)$"
                    }
                ],
                "errorMessage": "Paternal ID must be provided and cannot contain spaces. If no paternal ID is available, use 0.",
                "meta": ["paternal"]
            },

Seems risky having to keep track of "0" or 0.

@jemten
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jemten commented Oct 31, 2024

Yeah, the neater solution would probably be to fix this is in the schema. Need to run some tests to verify

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jemten commented Oct 31, 2024

Keep running into:

ERROR ~ Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --input (https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_single.csv): Validation of file failed:
	-> Entry 1: Error for field 'paternal_id' (): Value is [integer] but should be [string]
	-> Entry 1: Error for field 'paternal_id' (): Paternal ID cannot contain spaces
	-> Entry 1: Error for field 'maternal_id' (): Value is [integer] but should be [string]
	-> Entry 1: Error for field 'maternal_id' (): Maternal ID cannot contain spaces

Don't think I can solve this right now, know to little about nf-schema 😅 . Would this solution be OK for now and then we try to work some more on the schema solution later?

@jemten jemten merged commit 2eae461 into nf-core:dev Nov 1, 2024
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@jemten jemten deleted the upd_fix branch November 1, 2024 12:57
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Error in UPD on single sample
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@jemten @fellen31