Nils Homer

@jkbonfield @jmarshall do you have any more guidance on this? We merged https://github.com/samtools/samtools/pull/1605 which supports the strand of the source molecule in the template:coordinate sort.

Another idea: the default delimiter be comma and then have a parameter to control the delimiter?

``` $ agc --version agc version: 1.5.0 ```

I can try to make a PR, a first for me for Go.

I have hit this race condition submitting a workflow per sample in succession.

You could use the `--retries` option globaly or the `retry` directive for specific rules, but this will retry regardless of the type of failure.

Looking forward to this so I can set config options as per https://github.com/chanzuckerberg/miniwdl/issues/570

If inputsFile is specified on the command line and manifest, the behavior is undefined. In this case, it’s not specified in the manifest, so I’d expect it to use the...

I prefer 2 as I have static genomic reference data which could be in the manifest, and per-run sample genomic data and metadata that need to be custom for each...

I think this also blocks running multiple workflows concurrently in the same context, since the MANIFEST.json with a per-workflow `inputFileURLs` specified in the MANIFEST.json is packaged with the workflow (workflow.zip)....