Run --nanopolish on already basecalled data

[hoelzer]

The help of poreCov states that it is possible to skip basecalling when providing FASTQ files and a sequencing_summary.txt via --nanopolish. However, for me, this results in:

Please provide a fast5 dir for nanopolish [--fast5]

Code used:

nextflow run replikation/poreCov -r 0.11.7 -profile local,singularity --cores 16 --max_cores 240 --krakendb GRCh38.p13_SC2_2021-02-08.tar.gz -w work-run382 --fastq_pass fastq_pass --update --output results-run382-nanopolish --primerV V4.1 --nanopolish sequencing_summary_run21-382.txt -resume

Is there maybe just a check still active that prevents this combination of inputs from running?

[replikation]

• --fast5 is missing. then it skips basecalling
• will improve help before release, added this info for search and closing this