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Check for CSV/TSV format #16

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pcrxn opened this issue Jul 15, 2024 · 1 comment
Open

Check for CSV/TSV format #16

pcrxn opened this issue Jul 15, 2024 · 1 comment
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enhancement New feature or request

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@pcrxn
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pcrxn commented Jul 15, 2024

Description of feature

The workflow currently returns a ERROR ~ Invalid CSV value -- offending line: error if a TSV file is provided to --input instead of a CSV file. For example:

ERROR ~ Invalid CSV value -- offending line: "S01Batch012022SPEIWastewaterReferenceSiteGillSwabOysterWildS1S34"	"S01_Batch01_2022S_PEI_WastewaterReferenceSite_GillSwab_Oyster_Wild_S1_S34_R1_001.fastq.gz"	"S01_Batch01_2022S_PEI_WastewaterReferenceSite_GillSwab_Oyster_Wild_S1_S34_R2_001.fastq.gz"

Make this error more verbose or implement a specific check for comma separation instead of tab separation.

@pcrxn pcrxn added the enhancement New feature or request label Jul 15, 2024
@pcrxn pcrxn self-assigned this Jul 15, 2024
@pcrxn
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pcrxn commented Sep 9, 2024

There doesn't seem to be an obvious way to change this error message at the moment, unfortunately. I'll continue to monitor nf-schema development to see if this can be made more verbose in the future.

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