bigbio / bigbio/quantms

Deprecate openms tsv as an option for SDRF input and allow csv AND tsv

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#638 7 comments 1 reaction 2 assignees Claimed by @jpfeuffer View on GitHub
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Nextflow
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Description

A lot of plugins and other systems interfacing with nextflow require or default to creating samplesheet inputs as CSV for nextflow/nf-core pipelines. And cloud storage interface like Seqera Datastudios and Explorer have special rendering cases for CSV and TSV only.
In general I think the nf-core way is to have only ONE schema for the input parameter.

Therefore I think we should:
- deprecate allowing two formats (i.e. deprecate the openms schema)
- revert or only additionally allow .sdrf
- definitely allow csv and tsv as alternative suffixes

@ypriverol

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