Automatically mount non-standard directories

[nebfield]

Description of feature

The current approach of a python CLI application parsing a samplesheet doesn't work well if the container doesn't see the files on the host filesystem. This can happen if the files are "far away" or in non-standard directories (e.g. /scratch/). The problem is mostly triggered on HPCs with the singularity or apptainer execution profiles.

Two possible approaches:

• Stick with a (modified) python application and dynamically edit containerOptions
• Parsing samplesheets is pretty straightforward, implement in groovy and take advantage of nextflow autoMounts

The groovy approach is more portable across cloud executors / HPCs / object storage.

[nebfield]

closed by #244