search

nf-core / vipr

Assembly and intrahost / low-frequency variant calling for viral samples
https://nf-co.re/vipr
MIT License
14 stars 12 forks source link

params.tracedir in nextflow.config #29

Closed Ritzttk closed 5 years ago

Ritzttk commented 5 years ago

When I run the pipeline, I found the error : ${params.tracedir} is not found I don't find any record which has related to tracedir. So I added the value of tracedir like outdir

params {
    // defaults. best not changed
    version = '1.0-dev' // Pipeline version
    container = "nfcore/vipr:${version}" // for GIS translated into conda env name!
    nf_required_version = '0.30.2' // Minimum version of nextflow required
    outdir = 'results'
    tracedir = 'results'
    // Pipeline options
    skip_kraken = false
}

It worked but is it wrong ?.

Thanks, Kien

ewels commented 5 years ago

Hi @Ritzttk,

You are completely correct. Apologies, what you're seeing is why this pipeline is classed as under-development 😉 Much of the boiler plate code has been written by @andreas-wilm already but I don't think it's been tested much (or at all in its current state).

I'll fix this and a bunch of other stuff in a PR now, so that at least the automated tests should pass.

Phil

Ritzttk commented 5 years ago

@ewels Thanks for updating. I am using this pipeline for our unit. I start to set up. Hope that I am not bothering you too much Kiên

ewels commented 5 years ago

No, not at all! It's great to have you on board and using the nf-core pipelines! It's also nice to have an excuse to drive development on projects 😉

ewels commented 5 years ago

Hi @Ritzttk,

This should hopefully be resolved now. Please try pulling the latest version of the code and try again. Let's see what the next bug is! 😉

Phil