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Allow ingest-fastq to match filenames to a specified column of the assay table #198

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Nicolai-vKuegelgen opened this issue Nov 2, 2023 · 0 comments · Fixed by #203
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@Nicolai-vKuegelgen
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Is your feature request related to a problem? Please describe.
Incoming fastq files often have names based in sample_ids from the corresponding sequencing unit that do not match the sample or extract names in Sodar. Currently these secondary ids are often already placed in utilitary columns somewhere in the assay sheet (i.e. "Folder Name"), but can not be used for a Sodar-first fastq intake.

Describe the solution you'd like
A '--match-column {X}' option for cubi-tk sodar ingest-fastq that then matches file or sample names against that column X of the assay table and allows detemination of the irods-collection name based on a (default) column matching the irods collection names.

Describe alternatives you've considered
This is the easiest solution I can think of to enable a Sodar-first workflow with non-matching filenames. A current workaround- which is not Sodar-first - is to start ngs_mapping workflows that create input file links matching the library names of Sodar.

Additional context
Probably also allows closing of #4

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