DxNextflowWES

Genome Diagnostics Nextflow WES workflow

Get submodules, such as NextflowModules and CustomModules and install OpenJDK and Nextflow

sh install.sh

Running WES workflow

nextflow run WES.nf -c WES.config --fastq_path <fastq_dir_path> --outdir <output_dir_path> --email <email> [-profile slurm|mac]

Running WES Fingerprint workflow

nextflow run WES_Fingerprint.nf -c WES.config --bam_path <bam_dir_path> --outdir <output_dir_path> --email <email> [-profile slurm|mac]

Create Kinship container

guixr pack -f squashfs -RR -S /bin=bin king plink-ng vcftools@0.1.14 bash glibc-utf8-locales tzdata coreutils procps grep sed bootstrap-binaries
cp change/to/guix/path.gz.squashfs kinship.gz.squashfs
unsquashfs kinship.gz.squashfs
chmod -R 0775 squashfs-root
singularity build kinship.sif squashfs-root