Rnaseq: Can't stage file rfam-5.8s-database-id98.fasta

[paulklemm]

I'm running the nf-core/rnaseq pipeline in version 1.4.

Only when I enable --removeRiboRNA I get the following error:

Error executing process > 'sortmerna_index (rfam-5.8s-database-id98)'

Caused by:
  Can't stage file https://raw.githubusercontent.com/biocore/sortmerna/master/rRNA_databases/rfam-5.8s-database-id98.fasta -- reason: Unable to access path: /biocore/sortmerna/master/rRNA_databases/rfam-5.8s-database-id98.fasta

It appears that the link to the rRNA database is dead.

[apeltzer]

Yes, unfortunately the database location has been moved recently. This has been mentioned somewhere (can't find the link atm) but nobody so far fixed it for the next release.

[apeltzer]

Should be fixed in dev can you try? -r dev should run the dev branch.

[paulklemm]

Thanks! Cool, I have some new data to analyze anyway, can try it out in this context.

[paulklemm]

There seems to be a problem in dev mode at the moment.

Launching `nf-core/rnaseq` [stoic_minsky] - revision: 4b17f39ec3 [dev]
Unknown config attribute `params.igenomesIgnore` -- check config file: /home/pklemm/.nextflow/assets/nf-core/rnaseq/nextflow.config

I've already removed ~/.nextflow, but it didn't fix the error

[ppericard]

Should be fixed for good by #448