set of helper tools for the assembly of the different elements in the RELECOV platform (Spanish Network for genomic surveillance of SARS-Cov-2) as data download, processing, validation and upload to public databases, as well as analysis runs and database storage.
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Changing how analysis_date is collected from variants_long_table #266
Right now, when read-bioinfo-metadata is executed for viralrecon, the analysis_date field is extracted from the name of the variants_long_table file using the following regex variants_long_table_YYYYMMDD.csv. This is not very convenient as this is not its name by default and this information can be extracted from other more reliable files like pipeline_info/execution_trace*.txt which the date of the execution of each process in column 7 (name: submit)
Shettland
commented
1 month ago
Right now, when
read-bioinfo-metadatais executed forviralrecon, the analysis_date field is extracted from the name of the variants_long_table file using the following regexvariants_long_table_YYYYMMDD.csv. This is not very convenient as this is not its name by default and this information can be extracted from other more reliable files likepipeline_info/execution_trace*.txtwhich the date of the execution of each process in column 7 (name: submit)