PhilPalmer

Hi @marcovth, Sorry for the slight delay in response. I believe the issue is that you are not specifying a the `--bed` parameter for a BED file which is required...

Hi @cm760, Thanks for using the pipeline, sorry it's not working as expected. Unfortunately I haven't seen this error message before. Are you running it with any profiles? If not...

No worries I just spotted that your BED is compressed which may be causing the error. Can you please try uncompressing it & rerunning the command

Hi, sorry for the late response. Can I ask what is in your `prince.config` file? Also, I don't think this is causing the error but how come you're not using...

Are you able to send me the files to test with? Are they small and/or publically available?

Hi Harshil, Sorry for the late reply & thanks for the example link. It would definitely be great to add this. I hope to get round to doing this soon

Hi @moldach, sorry for my late reply on this I think this is the same issue as #13 This is an error in the documentation as Singularity Hub isn't really...

Hi @marchoeppner, > Currently, the pipeline uses "*.bam" to find input files. This is only when using the `--bam_folder` parameter. You could try using to the `--bam` parameter to specify...

Hi @kokyriakidis, 1. I have tried updating the pipeline. It wasn't working with the test data for some reason though. If you also want to try it out I pushed...

Hi, Sorry for the late response. In theory, it should be as simple as just updating this [one line](https://github.com/nf-core/deepvariant/blob/master/environment.yml#L9). However, when I tried updating the version to 0.72 the pipeline...