geertvandeweyer

I compiled and tested this, and it works correctly. As I'm not familiar with java/scala, I cant provide a full review unfortunately. I did notice some warnings when starting cromwell,...

Hi @henriqueribeiro , Do you think I can compile this branch with functionality of the latest cromwell release (77) ? I'm now using the branch based on cromwell 58, but...

Also have this error, using Cromwell 52, installed using this manual : https://aws-genomics-workflows.s3.amazonaws.com/Installing+the+Genomics+Workflow+Core+and+Cromwell.pdf logs say : fetch_and_run.is is a directory.

> Also have this error, using Cromwell 52, installed using this manual : > > https://aws-genomics-workflows.s3.amazonaws.com/Installing+the+Genomics+Workflow+Core+and+Cromwell.pdf > > logs say : fetch_and_run.is is a directory. Extra info : cloning job...

Old question, but on AWS, try the AWS-tailored fork : https://github.com/henriqueribeiro/cromwell/blob/develop_aws/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md This issue is handled there.

Old question, but on AWS, try the AWS-tailored fork : https://github.com/henriqueribeiro/cromwell/blob/develop_aws/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md This issue is handled there by correcting the multipart size in cromwell to match the AWS defaults

Yes, I would benefit from this :-) Cutadapt is the first step in our WES and WGS workflow on AWS. The massive staging of hundreds of FASTQ files when starting...

> I propose using smart_open with `ignore_extension` and then passing the filehandle to xopen. Xopen does not support filehandles yet. But it should be possible. Especially since the latest refactorings...

I've made some changes to xopen to support passing open filehandles. It's this PR : https://github.com/pycompression/xopen/pull/150 Once that is active, the current cutadapt PR can be re-evaluated. I've tested it,...

We occasionally see the same issue of lingering volumes. I'm wondering if you can either add the retry around the attach-volume and modify-instance-attribute, like it's used around eg the create-volume...