Merge pull request #17 from cokelaer/main

Update to use new layout

Merge pull request #11 from cokelaer/main

hotfix to use on HPC clusters

Merge pull request #9 from cokelaer/main

Use new sequana_pipetools framework(click)

Merge pull request #8 from cokelaer/main

Use sequana_wrappers from the config file

Update README.rst

Merge pull request #5 from cokelaer/main

update apptainers

Merge pull request #4 from cokelaer/main

Update pipeline to set singularity

Fix config file

Fixing pipeline for the --rRNA-file case

Fix sample names having same output name