BioWDL's repositories
ngs-performance-choices
Which tools to choose based on various performance metrics.
prepull-singularity
A tool for pulling singularity images in HPC environments.
pipeline-template
A pipeline template for modular pipelines
singularity-permanent-cache
Creates a permanent cache for singularity images on disk.
bam-to-gvcf
A BioWDL workflow for generating gVCF files from BAM files.
biowdl.github.io
The BioWDL organisation github.io site.
sequence-classification
A workflow for processing metagenomics data sets using Centrifuge. Category:Single-Sample
PacBio-subreads-processing
A Workflow for preprocessing PacBio reads. Category: Multi-Sample InDevelopment
all-pipelines
Contains all biowdl pipelines for maintenance purposes
biowdl-docs-theme
A theme for the BioWDL docs.
biowdl-input-converter
Converts sample configuration files into WDL structs in JSON format.
cnv-calling
Biowdl pipelines for CNV calling. Working from indexed bam files.
cromwell-resource-crawler
Crawl a cromwell-executions directory and report the used resources.
docker-bowtie-picard
A docker container with bowtie and picard
docker-bwakit
Container with BWA-kit and samtools
docker-bwamem2-kit
A docker container with bwa-mem2, bwa kit and samtools
docker-chord-mutsigextractor
A docker image containing CHORD, mutSigExtractor and the extractSigPredictHRD Rscript from Hartwig Medical Foundation's pipeline5 (https://github.com/hartwigmedical/pipeline5)
docker-clever-toolkit
Clever-toolkit patch
docker-curl
A debian container with curl installed.
jointgenotyping
A BioWDL workflow for generating a multisample VCF file from gVCF files.
minimal
Minimal is a Jekyll theme for GitHub Pages
PacBio-variantcalling
Variant calling workflow for targetted PacBio read data. Category:Multi-Sample
Testathon-2020
Repo For the WDL Testathon held February 18 - 19, 2020