I make use of cromwell in server mode to execute bioinformatics data processing pipelines written in widdle (.wdl = workflow description language). The machine from which I submit workflows is not the same as the machine that hosts the cromwell server (so a remote cromwell server). The input files for the workflow I want to submit are stored on the machine from which I submit, and they need to be available on the cromwell server machine? Should I first copy my files and then submit the workflow? Or is there a way to submit the workflow and let cromwell automatically copy the input files over?
Hi Geraldine (I think??), How do I make the cromwell server machine recognize the client/submission machine's file system? For example, do you recommend to to make my data directory on the client shareable over the network (SMB/CIFS), or can I adapt the URI string in my input file to something that will tell cromwell server to copy via ssh (e.g. ssh://client.machine.name/full/path/to/file.fastq)? Do I have to change anything in the cromwell configuration (there is a filesystem block)?
BTW, since the bioinformatics user base on biostars is 10 times larger then on bioinformatics.stackexchange.com I would recommend to move here :-)