Revise 'input_check' to 'input_assure'; enforce JSON key alteration to match the sample ID if a mismatch is detected #13
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…o match the sample ID if a mismatch is detected
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emarinier
requested changes
Jun 6, 2024
workflows/gas_nomenclature.nf
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| throw new RuntimeException("Pipeline exiting: sample with ID ${meta.id} does not have matching MLST JSON file.") | ||
| } | ||
| } | ||
| match.view() |
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Do we want to leave the .view() in or was this for debugging?
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Haha - I had used it for debugging.
Although highlighting this also made me realize that we no longer need to store the id_match boolean in the meta data as we won't be removing any samples from the analysis.
I have updated the python code, the workflow, and the input_assure process to simplify this here: 95e40f6
workflows/gas_nomenclature.nf
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| profiles = match.branch { | ||
| query: !it[0].address | ||
| } |
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Is this for only querying profiles that have don't already have an address?
emarinier
approved these changes
Jun 7, 2024
apetkau
requested changes
Jun 7, 2024
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This is amazing @kylacochrane 😄 . Thanks so much.
In addition to the in-line comments, could you fix the failing test prior to us merging the PR.
…n provided MLST JSON file(s)
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The following tests have been replaced or added:
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apetkau
requested changes
Jun 13, 2024
apetkau
requested changes
Jun 14, 2024
apetkau
approved these changes
Jun 14, 2024
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This is amazing @kylacochrane . Thanks so much for all your hard work 😄
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This PR resolves an issue that arises when a
.mlst.jsonfile, generated byLocidex, retains the original IRIDA Next sample identifier after a sample is cloned into a new project, leading to a mismatch in identifiers.To address this, the PR alters the previous
input_checkprocess, which now reads the.mlst.jsonfile fromLocidexand if the sample identifier does not match the JSON key, it is overwritten to ensure consistency.The process has been renamed to
input_assurefor clarity.An
error_report.csvis generated to identify any samples where the JSON key has been forcefully altered and discloses whether they are a query or reference sample in the pipeline.Info on added tests can be seen below in a separate comment.