offline usage

[anoronh4]

we need to prepare for offline usage in forte. we should expect that the clinical can cache or store any reference files to local storage, but any per-sample processes should be executable in an offline manner. There is some guidance from nf-core on offline usage

a few to do items:

• AGFUSION_DOWNLOAD: add storeDir option
• ARRIBA_DOWNLOAD: add storeDir option
• Add local configurations for raw reference files such as the fasta, cDNA, etc. We might consider a run option specifically for downloading.
• test using NXF_OFFLINE='TRUE'
• Create a CI test for NXF_OFFLINE

[anoronh4]

storeDir has been added for AGFUSION_DOWNLOAD and ARRIBA_DOWNLOAD. the NXF_OFFLINE setting turned out to not help us because the setting doesn't do what we thought, so the clinical team is doing all offline testing and configuration.