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TMB #616
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TMB #616
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Hi @FriederikeHanssen,
should be
with small 'c' |
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Ok this is starting to take shape. A couple of things that I could use help with:
1 & 2 maybe @apeltzer @tomgutman have any advice?
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For 3.) --> maybe somehing like "downstream-metrics"? :-) |
I'd even go just for |
Hello, unfortunately I don't have any expertise in VEP, strelka and freebayes. So I can't really help on that. =/ |
I'll prio the generation of the YAML files soon and will either find some time myself or have someone look into it. |
#495
Coming up with a POC for the tmb support:
Idea is to keep all relevant config files for the tmb tool in our own assests folder (or any other that we can control for now). Otherwise we are dependent that all of the tools that we would like to support will get added & released upstream. (Over time of course we could contribute them).
For all vcf files the variantcaller & annotation tool needs to be tracked in the meta map. We are already doing this for the variantcallers anyways. So this should be a small and easy change.
Last but not least the respective file can be retrieved with a groovy function for the proper combination.
Now of course we need to start generating all the db and var config files.
I am not sure yet how we could possibly handle users overwritting the config file. From where I stand at the moment we would need a parameter with which you can pass multiple files with a key...