marade

prohibitively slow performance

9

Testing for #9, the good news is using the --compliant switch for PROKKA apparently allows the script to continue beyond where it would previously crash, but then clinker engages in...

Due to Spades bug #863, conda.config does not work for MUFFIN

1

https://github.com/ablab/spades/issues/863 Until Spades 3.15.4 is released, it works properly with these changes: withLabel : spades { conda = 'bioconda::spades=3.15.3'} withLabel : python38 { conda = 'python=3.9 '}

For issue #250

Neighborhood based paralog splitting does not finish

2

For ~200 ~6Mb bacteria genomes, the neighborhood based paralog splitting step alone is taking over 24 hours on a c5.2xlarge EC2 instance, while the previous steps finished in a timely...

``` --- mlst.py 2023-04-06 20:38:09.323863921 +0000 +++ mlst.py 2023-04-06 20:37:46.011441012 +0000 @@ -158,10 +158,10 @@ return None else: dfblast = dfblast.join( - dfblast['sseqid'].str.split('.', 1, expand=True). + dfblast['sseqid'].str.split(pat='.', n=1, expand=True). rename(columns={0:...

--output_file does not work properly

5

Specifying an output directory with a relative path causes errors, e.g. this fails: $ mkdir genovi $ genovi -o genovi/blah ... Parsing path input with Pathlib Path(args.outfile).absolute() or os.path.abspath(args.outfile) would...

--title 'filename' does not work

8

SVGs and PNGs that are generated have "filename" in the center of the image.

hts_SuperDeduper should mark duplicates by default, not remove them

6

Picard MarkDuplicates, SAMTools markdup, SAMBlaster, and others all mark duplicates instead of removing them. This is the canonical, expected behavior of such utilities, and yet hts_SuperDeduper lacks even an option...

Hi. Thanks for this excellent package. I'm wanting to do a merge that is dependent on a second, unrelated set of intervals. If both the r- and q- intervals will...

Please document the program properly, step by step

2

The current documentation says we need query files and a config file in certain formats, but when I execute `mora --help` there are no flags for those. Some of the...