Check to ensure sample IDs match MLST.JSON keys #9
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… to mlst.json keys
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Encorporates new changes from filter-new-address
apetkau
requested changes
May 16, 2024
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This is amazing. Thanks so much @kylacochrane 😄 .
In addition to what we talked about I had a few other comments.
Made changes to the FILTER_QUERY script (csvtk)
Updated processes and workflow related to input sample checking
apetkau
requested changes
May 17, 2024
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This looks great. Thanks so much for your work @kylacochrane 😄 . Just two smaller comments.
modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
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Uploading files for new integration tests
apetkau
approved these changes
May 22, 2024
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This looks great. Thanks so much for all your hard work on this @kylacochrane 😄
| sample,mlst_alleles,address | ||
| sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/add_tests/tests/data/reports/sampleF.mlst.json, | ||
| sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1.1.1 | ||
| sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/add_tests/tests/data/reports/sample7.mlst.json,1.1.1 |
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As a note, once this PR is merged you'll have to update the URL here to point to dev. You can just directly commit that to the dev branch.
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This PR verifies that the sample IDs in the input samplesheet align correctly with their corresponding keys in the MLST JSON file.
INPUT_CHECK- verifies the sample ID and JSON key matches; outputs and maps the boolean value to the sample metadata; generates error_report.csv if applicableNOTE: See #10 for the addition of integration tests