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

Is your feature request related to a problem? Please describe.
While currently not used in the field (AFAIK) might be worth including bcftools stats for getting statistics on VCF files from genotyping. This would help for genotyping assessiment when not using MultiVCFAnalyzer (which is only really used in aDNA pathogen work).

It would be a simple process, with input channel being VCFs and

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

I am using the offline version of hlatyping pipeline, when I run the pipeline using the following command in lsf script I get the error : .command.sh: line 2: configbuilder: command not found

Command used to run the pipeline:
nextflow run /nf-core-Pipelines/nf-core-hlatyping-1.1.5/workflow/ -profile singularity -with-singularity nf-core-Pipelines/nf-core-hlatyping-1.1.5/singularity-images/

You're probably already working on this, but would it be possible to add CellRanger to nf-core/scrnaseq to perform alignment and preprocessing? If there is interest I would be happy to create a PR to dev with cellranger count output filtered_feature_bc_matrix that is processed by seurat.

We could also overwrite the experimental design generated from the SDRF but I don't know if that gets even more confusing.
Maybe in the long run we even deprecated the "--expdesign" parameter and require an SDRF? But the "--input foo.mzML --expdesign des.tsv" is just very convenient for quick analyses.