Nextflow GATK4 Germline pipeline for CMBG @2024

Make sure to get the correct config parameters. This is a private repository, you will need to create secrets to pull this repository by Nextflow:

append to ~/.nextflow/scm: providers { github { user = 'UCO' password = 'YOUPERSONALTOKEN' } }

If your docker image is private and hosted on Gitlab Muni:

Run docker login registry.gitlab.ics.muni.cz:443 -u -p on an ubuntu machine. Find the ~/.docker/config.json file. Run base64 config.json and copy the output into dockerconfig-secret.yaml (in git repo). Finally run kubectl --namespace [your new namespace] apply -f dockerconfig-secret.yaml to add the secret to the kuba cluster. This secret has to be added to nextflow.config: process { pod = [[imagePullSecret:'gitlab-svaton-secret'], ...] }

Samplesheet

The pipeline takes .json samplesheet in this format: { "samples": [ { "run": "Next_qJ_MGI", "name": "dHL2308qJ" } ] }

Optional parameters

The pipeline takes .json samplesheet in this format: --skipBQSR to skip recalibration of .bam files (save considerate amount of resources and time) --skipVQSR to skip recalibrating of .vcf files

@Jan Svaton 2024