These are chat archives for nextflow-io/nextflow

21st
Oct 2017
Bo
@wenbostar
Oct 21 2017 05:50
Does anyone know how to solve this problem? https://gist.github.com/wenbostar/d856601c471b6e0881c3df0d8fc1c60a
Paolo Di Tommaso
@pditommaso
Oct 21 2017 08:37
This is not a NF error, it's a problem with the GATK Docker container you are trying to run
moreover NF has built-in support for container, therefore you don't need to directly use the docker command
Alexander Peltzer
@apeltzer
Oct 21 2017 13:37
They had some issues with their native C code loading library in GATK 3.7 and GATK 3.8
Especially with the "NativeLibraryLoader"
Should be fixed with GATK 3.8 nightlies later than 2017-09-29
Bo
@wenbostar
Oct 21 2017 16:15
@apeltzer is there a example to show to gatk in docker in NF?
Paolo Di Tommaso
@pditommaso
Oct 21 2017 16:46
Have a look here
Bo
@wenbostar
Oct 21 2017 18:27
@pditommaso , thank you very much. Here is my nf script: https://gist.github.com/wenbostar/05b07612259011b4beca091b1327cf1c
It looks like the docker is not used by NF.
I can use this command line in the Linux system: docker run broadinstitute/gatk-nightly java -jar gatk.jar MergeSamFiles
USAGE: MergeSamFiles [arguments]
Bo
@wenbostar
Oct 21 2017 18:36
@pditommaso , I just checked the example: https://github.com/CRG-CNAG/CalliNGS-NF. It doesn't use gatk by docker.