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outputDir ties running RNA-seq to local file system - support for cloud file systems #74
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I'm not too familiar with the Google Cloud infrastructure or wdl-runner. Does the The file in question is actually an optional output, which is not generated by default, so it's a bit odd it's saying a "Required" file output is missing. Perhaps this is an issue with wdl-runner's localisation (maybe it doesn't support optional outputs). FYI We have tested this pipeline on AWS, where it ran (mostly) without issue. The only issue we had there was a bug in cromwell which has been fixed to my understanding. |
Hello @DavyCats - Ends up there are some utilities that are dealing with the paths quite nicely - so the error that I point out above was actually solved by editing 'Boolean createMd5File = true' instead of false - wherever I found it defined. |
Ah right, in that case setting |
Hello @DavyCats - I pretty much have it working now - except for variant calling. I've you'd like I can send my changes to you. A summary of changes are:
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Thanks for sharing!
Did editing the samplesheet to contain these paths not work?
I'm not sure what's going wrong here either. Does this file |
I'm trying to get this running on Google Cloud Platform using https://github.com/broadinstitute/wdl-runner
Unfortunately, the outputDir is pervasive throughout the WDL files and seems to be a show stopper.
I've modified some code to ignore Rna3PairedEnd.yml and that's worked.
But now the issue is with output files and their location.
Now, I'm getting errors like:
Required file output '/cromwell_root/./samples/rna3-paired-end/rna3-paired-end.markdup.bam.md5' does not exist.
Which, on GCP, it wouldn't.
This issue is for an 'enhancement' to support cloud file systems.
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