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Double quotes in queries in input causes parsing errors with the new nf-core template #108

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zachary-foster opened this issue Oct 31, 2024 · 0 comments
Open

Double quotes in queries in input causes parsing errors with the new nf-core template #108

zachary-foster opened this issue Oct 31, 2024 · 0 comments
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@zachary-foster
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This happens even though check_samplesheet.R replaces double quotes with single quotes, because this new check happens before. Errors like this happen:

ERROR ~ Invalid CSV value -- offending line: """Phytophthora""[Organism] AND ""wgs""[Strategy] ",3

 -- Check script './subworkflows/local/utils_nfcore_pathogensurveillance_pipeline/../../nf-core/utils_nfschema_plugin/main.nf' at line: 39 or see '.nextflow.log' file for more details
@zachary-foster zachary-foster added the bug Something isn't working label Oct 31, 2024
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