It would be nice to add a params to choose the VEP genome assembly.
In most cases it is the --genome params, but I'm assuming it'll be easier to control if we have that as a separate params.
For example, it's currently not working with the --genome custom setting.

Hi,

The time for fastqc is not enough...
I'm getting the following error:

Error executing process > 'fastqc (TBR532u)'

Caused by:
  Process exceeded running time limit (2h)

Command executed:

  fastqc --quiet --threads 1 TBR532u.R1.fq.gz TBR532u.R2.fq.gz

Command exit status:
  -

Command output:
  (empty)

Work dir:
  /path/to/work/68/387258828eecd198130d8230217c21

Indentation: Sometimes tabs have been used, sometimes spaces (maybe a vim thing). I think it would be best with an indentation of two spaces.

--manifest: It says "table" where it should say "tab" and the rest should be checked to be grammatically correct.

I think there may be other mistakes, so a read through could be worthwhile.

Hi there,
I wonder if it would be possible to add a feature in the pipeline allowing libraries made with different adapter sequences to be processed in the same run.

For example, my colleagues and I are often working with a mixture of Illumina and BGI (4 channel) sequencing data and it would be cool to be able run these data together, instead of having to run adapter removal separately for eac

I think it would be good to have module for ensembl-vep

I'm getting an error when trying to pull with singularity (version 3.5.2-1.el7)

singularity pull --name nf-core-deepvariant.simg shub://nf-core/deepvariant

FATAL:   While pulling shub image: failed to get manifest for: shub://nf-core/deepvariant: the requested manifest was not found in singularity hub