Local Cromwell implementation of GATK4 germline variant calling pipeline

See the GATK website for more information on this toolset

Assumptions

• Using hg38 human reference genome build
• Running 'locally' i.e. not using HPC/SLURM scheduling, or containers. This repo was specifically tested on Pawsey Nimbus 16 CPU, 64GB RAM virtual machine, primarily running in the /data volume storage partition.
• Starting from short-read Illumina paired-end fastq ...

This is a Galaxy workflow that uses to convert the16S BIOM file to table and figures. It is part of the metaDEGalaxy workflow MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data.

A porting of the Trinity RNA assembly pipeline, https://trinityrnaseq.github.io, that uses Nextflow to handle the underlying sub-tasks. This enables additional capabilities to better use HPC resources, such as packing of tasks to fill up nodes and use of node-local disks to improve I/O. By design, the pipeline separates the workflow logic (main file) and the cluster-specific configuration (config files), improving portability.

Based on a pipeline by Sydney Informatics Hub: ...