Finlay Maguire
Finlay Maguire
Saw a few issues mentioning this so ran a quick update of the built-in dbs. Tested on the test files via fofn.txt (and an additional genome as these files didn't...
Hi, Don't suppose you know the releases/versions of lasagne, theano (and ideally pygpu) that the subcellular localisation code was originally written using?
If the exact same tool is run with different settings (but all the other metadata stays the same such as version) summarize falsely combines them e.g., running RGI on contigs...
For the interactive report or tabular report possibly have an option to just summarise results (genome, gene, tool, versions, phenotype annotation) and the full genomics results (i.e., the whole spec...
To handle concerns raised by @cimendes in #39 and try and make issues with input selection clearer to users e.g., #54 we should add proper use of `logging` library, default...
`kma` silently fails when executed by `kmerresistance`: specifically no error just a non-zero exit code and no output. I can only reproduce this in the container (based off debian) and...
Making this an issue so I don't forget about it while I think about ways to implement it: - Add rule that runs `pangolin --update` before `pangolin` is run on...
The IonTorrent platform provides reads in an unaligned .bam instead of .fastq. Modify workflow to automatically convert supplied .bam to .fastq by adding a conditional to this rule: https://github.com/jaleezyy/covid-19-signal/blob/master/Snakefile#L245 (e.g.,...
Updated postprocessing to add scorpio calls to the HTML report.