Stephen Kelly

I needed this exact feature, hope it can get merged in soon. Thanks for implementing this :)

I think this might be related? similar issues; https://www.biostars.org/p/9468744/

So, one method I am using right now to avoid this issue, is to insert UUID's into filenames; ``` #!/usr/bin/env cwl-runner cwlVersion: v1.0 class: CommandLineTool baseCommand: [ "bash", "run.sh" ]...

should the standard be updated to include support for S3 protocol? It seems pretty widespread these days

I agree that something which integrates as cleanly as possible with the current Nextflow infrastructure would probably be best

It seemed to me that one of the challenges was just in writing the code the check the output of each file type. That's why in my example I did...

for reference, the method I hacked together with Python `unittest` was to just validate the exit status of the pipeline, and do custom parsing of the output files; https://github.com/stevekm/nextflow-ci/blob/master/test_nextflow.py https://github.com/stevekm/nextflow-ci/blob/master/test_flagstat.py...

You might try commenting out these two lines; https://github.com/stevekm/IGV-snapshot-automator/blob/d2c01a5d683ce29ba7c0a8920f563b467f924d32/make_IGV_snapshots.py#L223-L224 I had previously been using this method to obtain an open xvfb server number; https://github.com/stevekm/IGV-snapshot-automator/blob/d2c01a5d683ce29ba7c0a8920f563b467f924d32/make_IGV_snapshots.py#L120-L135 However I later found that many...

this whole process is a little tricky since it seems like different systems have slightly different versions of `xdpyinfo` and `xvfb-run` which can cause problems like this.

marking this as a bug that I should probably fix; just get rid of the old command that is not needed anymore