WDL + cromwell and remote server
Entering edit mode
2.7 years ago
c.clarido ▴ 80

Good day community,

I'd like to build a WDL SV calling pipeline that accepts BAM and reference files. I have the files in a remote server which I have mounted with sshfs in my local.

When I try to testrun the workflow, I get a warning that hardlinks can not be made. At the end, the run failed because there weren't enough space left anymore for other files. It seems that the reference file was copied but not the BAM file, the workflow tried to find the BAM but could not find.

Is there any way I can access the files from the remote server and use them in the workflow in my local computer?

Thank you in advance.

wdl cromwel pipeline sshfs • 753 views

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