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gbouras13 / hybracter

Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
MIT License
108 stars 8 forks source link

New parameter pointing to the raw data #76

Closed oschwengers closed 2 months ago

oschwengers commented 6 months ago

Hi George, thanks so much for this wonderful tool - I got awesome results so far!

I just thought about an additional --data parameter that would accept the path to a data directory where all the raw incoming reads are stored. By this, users don't have to put these often very long paths into the csv file which might be error prone and a bit inconvenient. So if there is a path provided via --data, the csv file will only contain the file names.

How about that? Thanks!

vdejager commented 2 months ago

Hi george,

is the --datadir option in 0.8.0 now mandatory? Whenever I use full paths in my sample.csv, hybracter complains that it cannot find the files. If I copy the files in my directory from where I run hybracter, it runs as expected. Note: I have to use the docker container on our HPC.

does the datadir option take multiple arguments? (to accomodate reads in different directories, e.g. nanopore in one, illumina in the other)

gbouras13 commented 2 months ago

Hi @vdejager ,

Do you mind sharing an error log? It was certainly not my intention for it to be mandatory. It could be container specific too, not sure.

It does not take multiple arguments, but that is a great idea to be honest - assuming this is a bug I have to fix, I'll think about implementing that.

George

gbouras13 commented 2 months ago

@vdejager, your request is implemented in v0.9.0. --datadir "longdir,shortdir" where the directories are separated by a comma should work

George