David Fischer

- add profile for `SGE` - add documentation in `README` and help message

GARD_detect HPC issues, closes #31

2

- changed /TEMPDIR from $(PWD) to `/tmp` because path was too long for MPI - copy `${aln}` to /TEMPDIR since `GARD` wasn't able to follow the symlink on the cluster...

GARD process fails if temp dir path for MPI is too long

3

Just ran into this issue while running with `singularity` on an HPC: ``` PMIx has detected a temporary directory name that results in a path that is too long for...

add fastcov module

2

## PR checklist Add nf-core module for fastcov coverage plotting tool. The module was tested with singularity and docker using the container provided by the tools dev. There is currently...

Question regarding GFF file generation

2

Hey, thanks for this nice pipeline! I'm running the pipeline with the `--list` argument providing a sample sheet to it to run on ~100 samples. But for all the viral...

Add VirSorter2 process as an alternative to VirSorter

3

Added [VirSorter2](https://github.com/jiarong/VirSorter2) as a new process that can be used instead of `VirSorter` using the new flag `--use_virsort2`, adapted the downstream processes (the `parse` process and GFF generation script) to...