Releases · replikation/poreCov

pangolin and nextclade version updates
automatically removing whitespace from files used as input for --samples
changed artics normalize to 500
some more verbose exit statements during guppy basecalling to better understand what might be "missing" dependency wise
set poreCovs parallel capabilities to "4" runs in parallel (default)
- should still work on "compute toasters"
more verbose error statements for inputs (e.g. if you miss adding the fasta file to the --fasta flag)
nanopolish skips basecalling if fastq data is provided, but this needs a sequence summary file in return (supplied via --nanopolish)
- error code added for this to explain the user what is missing
bug fix if internet is unavailable for "get latest poreCov release" functions

on startup the latest poreCov version available on Github is shown (#89)
summary report file is also saved as tsv and excel file ( yes excel ;) thx @RaverJay ) (#88)
nanopolish was added to poreCov, activate via --nanopolish if --fast5 is provided (#87)
pangolin version update
error exit message if --samples table is not able to be merged with any of the barcodes to rename them (#86)
warning message if not enough barcode reads are available in ALL of the run (#86)
- this appears if no genome reconstruction is starting - I did not add a "exit" so that read classifications and qc will finish for trouble shooting
reads files below 1.5 Mbyte are not removed if --samples is provided (should improve but not fix #92)
- the sample name merge will remove "faulty barcodes"
- still wip, the issue is that e.g. for one end demultiplexing other barcodes are appearing that are not used (e.g. barcode 96 due to the read errors)
- the sample file needs to be used in the final report to add "missing" barcodes

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