LIMS: Changes to make samplesheet compatible with pipeline#91
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niamhat wants to merge 2 commits intodevelopmentfrom
Open
LIMS: Changes to make samplesheet compatible with pipeline#91niamhat wants to merge 2 commits intodevelopmentfrom
niamhat wants to merge 2 commits intodevelopmentfrom
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Istaisa
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Feb 27, 2026
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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.
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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