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CRG-CNAG / CalliNGS-NF

GATK RNA-Seq Variant Calling in Nextflow
Mozilla Public License 2.0
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Documentation issue? #32

Open pieterlukasse opened 2 years ago

pieterlukasse commented 2 years ago

The documentation at https://github.com/CRG-CNAG/CalliNGS-NF/blob/master/docker/README.adoc states

A Docker container with all tools except the Genome Analysis Toolkit can be built from the Dockerfile present in this folder

However, the Docker file does install GATK as well in https://github.com/CRG-CNAG/CalliNGS-NF/blob/master/docker/Dockerfile#L46:

&& curl -fsSL https://github.com/broadinstitute/gatk/releases/download/4.1.1.0/gatk-4.1.1.0.zip > gatk-4.zip \

pieterlukasse commented 2 years ago

One related question I had was: can I configure different docker images, one for each step? Or am I limited to a single value for process.container in the config file?

pieterlukasse commented 2 years ago

Ok, I found the answer to my related question above: https://github.com/nextflow-io/nextflow/blob/master/docs/process.rst#container -> the container can be set individually for each "process". Maybe this is what should be done for the GATK process items in https://github.com/CRG-CNAG/CalliNGS-NF/blob/master/modules.nf