DrYak

> Hmm ok, thanks for that- I'll alter the directories. Since a few days, the latest version contains a few utilities that might help you automatically build this structure +...

Though you have managed to make it work, I would be interested in your YAML and TSV files (if you don't mind sharing them) so I can see what was...

Okay, I got what is happening (though I would need the content of the `samples.tsv` and a little bit more of the logs). The filtering step (PrinSeq) is misfiltering most...

> Your files are pair-ended and contain 100bp per read. > > By default, V-pipe assumes a length of 250bp. (and if you look a few lines higher in the...

@carolinasisco: > Hi, did you create this folder in your working directory? How are you running V-pipe? In general all the files need to go in the working directory: Either...

> I´m not giving the samples.tsv since is optional, I´m stating in the config file the datadir, Yes, specially since you're setting the read-length in your tsv: `read_length: 151`, you...

> but the pipeline has been showing a message of "Activating conda environment: /home/geninfo/msisco/V-pipe/workflow/.snakemake/conda/6b4b4f9b39457eac0d31ae59ec8c6ce6 for a few hours, without any changes.. is this normal? Yes, shorah doesn't output much on...

> I ran the pipeline successfully, it lasted around 18 days. Yes, it can take time. For future runs, I would suggest running it on the cluster or on a...

Hi! Currently, we don't trim primers yet. (the primers are only used for display on the visualisation, for now). It is a feature planned in the future. It will be...

Hi! Upgrading the configuration from the old [bespoke format based around Python classes](https://github.com/cbg-ethz/V-pipe/blob/master/rules/config_default.smk), into something [that actually use modern configuration format](https://github.com/cbg-ethz/V-pipe/pull/93) is on our todo list.