Benjamin Wingfield

You need to use `"` characters when using a wildcard, e.g.: ``` --scorefile "downloads/PGP000604/*.txt.gz" ``` Without quotes [your shell expands the wildcard character into a list of file paths, which...

Here's an example configuration file I use for UK Biobank on my HPC cluster: ``` process { errorStrategy = 'retry' maxRetries = 3 maxErrors = '-1' executor = 'slurm' withName:...

Closing this now. Please feel free to create a new issue or discussion if you have any more questions.

Thanks for the bug report. I've encountered this a few times before when Nextflow's `-resume` gets a bit confused. Does the problem still happen if: 1. You run the workflow...

Does the problem still happen if you set: https://github.com/PGScatalog/pgsc_calc/blob/96fbb2346978c12917d35dc68520a86a9f7b7cc0/nextflow.config#L306-L313 to `enabled = false`?

It might help to install Nextflow using your normal user outside of a conda environment. ``` $ curl -s https://get.nextflow.io | bash ``` and then run the Nextflow executable that...

Closing this now. Please feel free to create a new issue if you still experience problems.

The [calculator works best with cohort data that have been imputed](https://pgsc-calc.readthedocs.io/en/latest/how-to/samplesheet.html#samplesheet). If you have one sample per VCF then you should [merge your target genomes before using the calculator](https://pgsc-calc.readthedocs.io/en/latest/how-to/prepare.html). Multiple...

[WGS data can cause variant matching problems with the current version of the calculator](https://pgsc-calc.readthedocs.io/en/latest/explanation/match.html#are-your-target-genomes-imputed-are-they-wgs). The calculator works best with genotyping array data that have been imputed to increase variant density....

Closing this now. Please feel free to create a new issue or discussion if you have any more questions.