calc_heritability

This pipeline calculates both broad sense and narrow sense heritability and is used as the heritability calculator for CeNDR.

Usage on QUEST

# set up environment
module load python/anaconda3.6
source activate /projects/b1059/software/conda_envs/nf20_env
module add singularity

# run pipeline
nextflow run andersenlab/calc_heritability --vcf 20210121 --traitfile <path_to_file>

Usage on local machine (not QUEST)

Note: this pipeline requires previous installation of docker and nextflow

• By failing to specify a vcf, the pipeline will automatically download the current C. elegans release from CeNDR

# run pipeline
nextflow run andersenlab/calc_heritability --traitfile <path_to_file>

Usage on GCP/CeNDR

Provision a virtual machine from the existing template and connect with SSH, then switch to the root user and install the required packages:

sudo su
apt-get install docker.io git nano

Use 'nano' to create a *.env file (see: example.env) with variables pointing to your Google Storage locations:

nano test.env

test.env:

TRAIT_FILE="gs://elegansvariation.org/reports/heritability/kse_test_hert/ExampleTraitData.csv"
OUTPUT_DIR="gs://elegansvariation.org/reports/heritability/kse_test_hert2/results"
WORK_DIR="gs://nf-pipelines/workdir/kse_test_hert"
VCF_VERSION="20210121"

docker run -i -t \
  --env-file test.env \
  andersenlab/calc_heritability:v0.1 \
  heritability-nxf.sh

You can also pass them in as part of the command:

docker run -i -t \
  -e TRAIT_FILE="gs://elegansvariation.org/reports/heritability/kse_test_hert/ExampleTraitData.csv" \
  -e OUTPUT_DIR="gs://elegansvariation.org/reports/heritability/kse_test_hert2/results" \
  -e WORK_DIR="gs://nf-pipelines/workdir/kse_test_hert" \
  -e VCF_VERSION="20210121" \
  andersenlab/calc_heritability:v0.1 \
  heritability-nxf.sh