vortexing

bcftools-docker

bwa-docker

cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

docker-conda-base

docker-gatk-samtools

gatk and updated samtools

docker-gatk-samtools-bcftools

docker-R-bioconductor

docker-samtools

docker-subset-bam

10x genomics subset bam docker setup/wdl

docker-umi-star-sam

umi-tools, STAR aligner, samtools

docker-vartrix

10x genomics vartrix docker/wdl setup

easybuild-life-sciences

Howto and implementation documentation

gatk

Official code repository for GATK versions 4 and up

ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

R-fetch-and-run-docker

s3tagcrawler

search s3 based on tags

slurm-examples

examples of using slurm in life sciences workflows using posix file systems and object storage

star-docker

Docker container with STAR and samtools

strelka-docker

strelka in docker

umi-tools-docker

vortexing.github.io

A short landing page for me.

wdl

Workflow Description Language - Specification and Implementations