New Resfinder v4.5.0

[DanyMatute]

The newer version of Resfinder 4.5.0 produces NA and NA..NA when --inputfastq flag is implemented, and this flag is used to run the KMA. These are removed as it clashes with the expected variable type "int"

[fmaguire]

Hi @DanyMatute this is great, thanks! Do you have a ResFinder v4.5 output on hand I can add as a testcase? No worries if not!

[DanyMatute]

Hello @fmaguire
here is a fastq resfinder 4.5.0 output
python3 -m resfinder --inputfastq read1.fastq read2.fastq --species species --disinfectant --acquired --point --ignore_missing_species --outputPath read_output ~{'--min_cov ' + min_cov} ~{'--threshold ' + threshold}

ResFinder_results_tab.txt

and a fasta resfinder 4.5.0 output
python3 -m resfinder --inputfasta assembly.fasta --species species --disinfectant --acquired --point --ignore_missing_species --outputPath assembly_output ~{'--min_cov ' + min_cov} ~{'--threshold ' + threshold}
ResFinder_results_tab.txt

finally a fasta and fastq resfinder 4.5.0 output
python3 -m resfinder --inputfasta assembly.fasta --inputfastq read1.fastq read2.fastq --species species --disinfectant --acquired --point --ignore_missing_species --outputPath assembly_output ~{'--min_cov ' + min_cov} ~{'--threshold ' + threshold}
ResFinder_results_tab.txt

[fmaguire]

Amazing, I've just added some tests using your examples and will update the version shortly.