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License: MIT License
Genotype Imputation Pipeline for H3Africa
License: MIT License
Generate base images for the docker swarm nodes (probably ubuntu 16.04 based)
Get the basic Impute2 example running in NextFlow
move these to config
Line 133 in 149d31f
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!
Please send your ssh public keys to me ([email protected]) if you want to be able to log into the shells of the images.
Generate a debian package which deploys docker swarm to base images
The reference panels are built using a separate pipeline here
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
remove
Line 362 in 149d31f
Missingness was being filtered on chromosome level but that results in mismatched chromosomes. Disabled it here 20aed0c
write down the minimal steps for a minimal workflow
I am ok to run test pipeline, but when using my own config there was an errorERROR ~ Unknown method invocation
call on BigInteger type
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