h3abionet / chipimputation Goto Github PK

Hi! I noticed you are pulling your container (recipes here) and as Singularity Hub is not officially open yet, I'll please ask you to refrain from doing this. Thanks!

• check for 0/X genotypes

Generate base images for the docker swarm nodes (probably ubuntu 16.04 based)

move these to config

Get the basic Impute2 example running in NextFlow

Missingness was being filtered on chromosome level but that results in mismatched chromosomes. Disabled it here 20aed0c

Please send your ssh public keys to me ([email protected]) if you want to be able to log into the shells of the images.

write down the minimal steps for a minimal workflow

remove

The reference panels are built using a separate pipeline here

Generate a debian package which deploys docker swarm to base images

in main.nf line 267 create a channel of ref_panels. when using %s for string interpolation, %s is not replaced. would following code correctly create a channel of ref_panels?
inp = Channel.from(params.ref_panels) .combine(Channel.from(params.chromosomes.split(','))) .flatMap { ref_name, ref_m3vcf, ref_vcf ,chrm-> vcf = sprintf(ref_vcf, chrm) m3vcf = sprintf(ref_m3vcf, chrm) return [ [ ref_name, file(m3vcf), file(vcf)] ] }
thanks, Hongchen Zheng

I am ok to run test pipeline, but when using my own config there was an errorERROR ~ Unknown method invocation call on BigInteger type