Fredrik Boulund

Script to download everything from figshare

3

Torsten Seemann (@tseemann) suggested I share this script I wrote a while back: ``` #!/bin/bash # Download pre-made Kraken2 database based on GTDB r89 # https://github.com/rrwick/Metagenomics-Index-Correction # https://monash.figshare.com/articles/GTDB_r89_54k/8956970 # https://www.biorxiv.org/content/10.1101/712166v1...

Hi, I see some strange behavior, where the some of the output files don't have the prefix assigned via `-b`: ``` $ ls C1825_AAGACGA_L006.nobg.fastq $ nonpareil -s C1825_AAGACGCA_L006.nobg.fastq -f fastq...

Syntax errors in metacherchant.sh

1

There appears to be something wrong in the `metacherchant.sh` script on lines 23 and 24. Not sure if this affects how it works (haven't tried it yet). ``` $ bash...

I recently discovered that `krakenuniq` fails when the (paired) input files are symlinks: I'm running the latest version installed from conda ``` (krakenuniq) [boulund@c1hitachi10 kutest]$ krakenuniq --version KrakenUniq version 1.0.3...

Make possible to install using pip or conda

2

Are there any plans to make the tool installable via pip or conda?

Steffi suggested making it easier to find the versions used of everything

Remove str conversions in all rules

2

Snakemake should be Pathlib compatible across the board now, so it should be possible to remove all the superfluous str conversions in all rules.

Add SUPER-FOCUS

1

I've started working on adding [SUPER-FOCUS](https://github.com/metageni/SUPER-FOCUS) now that it's installable via conda. We will probably not implement automatic database downloading for SUPER-FOCUS to begin with, as I think the database...

Warn user if signalp is missing if prokka_gram is true

9

I would like BACTpipe to detect if `signalp` is missing if `prokka_gram` is set to true, and warn the user that prokka requires signalp if combined with the `prokka_gram` option...