jsalmingo-add parameter validation #277
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j2salmingo
changed the title
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The validation seems to be good, a couple of things:
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I've updated the comment label to use the appropriate directory, and added test cases with invalid config files and invalid input csv cases, as well as testing with YAML input. |
yashpatel6
approved these changes
Aug 18, 2023
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Generally looks good! Is this closing #239? I don't think any of the changes are relevant to that issue.
Also, if the standard csv has the BOM issue, can you update the original file /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/input/csv/a_mini_n2.csv?
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Oh, that's my mistake with #239. I confused nextflow-module/validate with nextflow-config. I shall edit and merge. |
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Description
Closes #260
Adds parameter validation
NOTE: The original input csv file contained a UTF-8 BOM which needed to be deleted in order to pass validation. Please see uclahs-cds/pipeline-Nextflow-config#27
Testing Results
BWA-MEM2 & HISAT2
BWA-MEM2 & HISAT2
For invalid cases to test validation, the following config files and input_csvs were used, located in the /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jsalmingo-add-parameter-validation directory:
a_mini_n2-picard-invalid-aligner.config
a_mini_n2-picard-invalid-dir.config
a_mini_n2-picard-misspelled-header.config
a_mini_n2-picard-no-fq2.config
a_mini_n2_no_BOM_invalid_dir.csv
a_mini_n2_no_BOM_misspelled_header.csv
a_mini_n2_no_BOM_no_fq2.csv
Checklist
I have read the code review guidelines and the code review best practice on GitHub check-list.
I have reviewed the Nextflow pipeline standards.
The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
I have set up the branch protection rule following the github standards before opening this pull request, or the branch protection rule has already been set up.
I have added my name to the contributors listings in the
manifestblock in thenextflow.configas part of this pull request, am listedalready, or do not wish to be listed. (This acknowledgement is optional.)
I have added the changes included in this pull request to the
CHANGELOG.mdunder the next release version or unreleased, and updated the date.I have updated the version number in the
metadata.yamlandmanifestblock of thenextflow.configfile following semver, or the version number has already been updated. (Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.)I have tested the pipeline on at least one A-mini sample with aligner setting to
BWA-MEM2,HISAT2, and both. The paths to the test config files and output directories were attached in the Testing Results section.