Feature request: publishDir, annotation , etc...

[lindenb]

Hi,

than you for this workflow ! I successfully ran it for 2000WGS ! However, I got a 'too many files open' for VCF_MERGE and I add to modify the 'script' section run bcftools merge by batch of 100 files.

The HTML output is really nice but as a bioinformatician it is less useful. I'd like to see the merge VCF file in the final output as well as a TSV file containing the haplogroups, the contamination status for each sample, etc....

Furthermore, in the VCF file, it would be useful to get the annotations (Expected,Local-Private, etc...) in the INFO/FORMAT .

Thanks !

[seppinho]

Awesome, thanks for testing!! All good points. Will work on that step by step. I probably start by fixing the merge problem and then go on to the VCF.