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Empty fields in CSV #67

Merged
merged 3 commits into from
Jun 3, 2024
Merged

Empty fields in CSV #67

merged 3 commits into from
Jun 3, 2024

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yashpatel6
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  • 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 or verified the branch protection rule following the github standards before opening this pull request.

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    metadata.yaml and the manifest block in the nextflow.config as part of this pull request, am listed
    already, or do not wish to be listed. (This acknowledgement is optional.)

  • I have added the changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

  • I have updated the version number in the metadata.yaml and manifest block of the nextflow.config file 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 config being added or modified. Outline the tests below.

Adding option to allow empty fields when parsing a CSV. Tested with metapipeline-DNA PR adding CSV support

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@nwiltsie nwiltsie left a comment

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As-is the parser isn't robust to quoted strings containing commas, but that is orthogonal to this change. Overall this looks good.

@yashpatel6
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Agreed, the current parser is fairly bare-bones and won't really handle cases with commas and such in quoted values

@yashpatel6 yashpatel6 merged commit be1eaf5 into main Jun 3, 2024
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@yashpatel6 yashpatel6 deleted the yashpatel-allow-empty-csv-fields branch June 3, 2024 17:18
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2 participants