A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

I'm running this pipeline on azure and 1 process (<https://github.com/nf-core/rnaseq/blob/master/modules/local/star_genomeparams_upgrade/main.nf|star_genomeparams_upgade>) is giving me trouble because azcopy (version 10.8.0) doesn't follow the symlinks.  The task succeeds but subsequent tasks fail because the symlinked files aren't copied to the output blob.  Has anyone ran into or resolved this issue yet?

I'll look at a fix.

But FWIW this error tells me that you're using `--genome` , which I'd REALLY recommend against: <https://nf-co.re/rnaseq/3.26.0/docs/usage#igenomes-not-recommended|nf-co.re/rnaseq/3.26.0/docs/usage#…>

The annotations there are hopelessly out of date. You should supply `--fasta` and `--gtf` from up to date sources <https://nf-co.re/rnaseq/3.26.0/docs/usage#igenomes-not-recommended|nf-co.re/rnaseq/3.26.0/docs/usage#…>

Thank you.  I'll make that change on my next run.