ERROR ~ Unknown config attribute: igenome_base

[mhebrard]

Hi, I try to use NGI-RNAseq for the first time, so I might forget something.

I am on windows and installed Singularity using vagrant I use vagrant to launch a linux machine with VirtualBox (Ubuntu 16.04) in this machine, I installed Singularity 2.4 and Nextflow 0.29.1 Then I run:

nextflow run SciLifeLab/NGI-RNAseq -with-singularity --genome GRCm38 --reads '/vagrant/Data/*_R{1,2}*.fastq.gz'

I get the trace

N E X T F L O W ~ version 0.29.1
Pulling SciLifeLab/NGI-RNAseq ...
 downloaded from https://github.com/SciLifeLab/NGI-RNAseq.git
Launching `SciLifeLab/NGI-RNAseq` [elegant_davinci] - revision: a21a1077ec [master]
ERROR ~ Unknown config attribute: igenome_base -- check config file: 
/home/vagrant/.nextflow/assets/SciLifeLab/NGI-RNAseq/nextflow.config

null

 -- Check '.nextflow.log' file for details

It looks like an issue with the variables that compose the URL to download the reference genome... do you have any advice ?

[ewels]

Hi @mhebrard,

Thanks for this - it's a known bug. We've actually moved this pipeline over to the new nf-core community here: https://github.com/nf-core/rnaseq (see http://nf-co.re). I fixed it in that version of the pipeline but haven't applied the patch here.

You're not the first to mention this, so I should really do a minor release here just fixing this bug. Then I should archive this pipeline and redirect to the new nf-core one.

Now I just need to remember how I fixed it..!

Phil

[ewels]

Closing this as we now have a release on the new nf-core pipeline, meaning that it's the recommended pipeline to use now (lots of other nice additions there too!).