LIMS: Changes to make samplesheet compatible with pipeline#91
LIMS: Changes to make samplesheet compatible with pipeline#91niamhat wants to merge 6 commits intodevelopmentfrom
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Istaisa
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This has been run successfully on the test run and produces the appropriate csvs for the additional referrals.
Could the selection of columns etc. be changed from a positional selection to a selection by column header instead? Then it can remain compatible with runs from both SHIRE and GLIMS - then we can deploy whenever but also retain the ability to rerun old runs once GLIMS is live.
| sample_id = line["Sample_ID"] | ||
| worksheet = line["Sample_Plate"] | ||
| sample_type = line["Sample_Type"] | ||
| description = line["Description"] |
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There was an issue when I first tried to run this where the sample headers for the SampleSheet on wren had a space after 'Description', so was getting a key error. I'm not sure what's happened with this as I tried re-downloading one from the samplesheet generator and no space. Have removed to run the rest of the code.
Istaisa
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Data from samplesheet is now parsed by column header instead of by position. Tested with both GLIMS and SHIRE samplesheets, compatible with both.
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Some columns and header in the new samplesheet have changed.
sample_type is now column 8 and worksheet is column 1.
Accounted for additional referrals to make their own csv per additional referrals. This is then handled in somatic_enrichment_nextflow https://github.com/AWGL/somatic_enrichment_nextflow/pull/101
Currently tested on 260102_A01771_0767_AH5VGLDRX7
/data/output/validations/lims_tests/somatic_enrichment_nextflow_test