biowdl Goto Github PK
Name: BioWDL
Type: Organization
Bio: Bioinformatics workflows and tasks, written in WDL.
Location: Leiden
BioWDL's Projects
docker-pave
A docker image for hartwigmedical/hmftools' pave
docker-peach
A docker image for hartwigmedical's PEACH.
docker-protect
A docker image for hartwigmedical/hmftools' protect
docker-pyyaml
A docker image based on py3.6-slim that includes pyyaml.
docker-virus-interpreter
A docker image for hartwigmedical/hmftools' virus-interpreter
docker-wiseguy
Docker container for https://github.com/sndrtj/wisecondor
expression-quantification
A BioWDL workflow for quantifying expression. Category:Multi-Sample
gams
Genomic Annotation of Metagenomic Sequences.
gatk-cnvcalling
The BioWDL implemention of the GATK CNV calling workflow. Category:Multi-Sample
gatk-preprocess
A BioWDL workflow for preprocessing BAM files for variantcalling. Based on the GATK Best Practices. Category:Single-Sample
gatk-variantcalling
A pipeline that calls variants on a group of BAM files. Category:Multi-Sample
generate-test-data
Pipelines for generating biowdl test data.
germline-dna
A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample
jointgenotyping
A BioWDL workflow for generating a multisample VCF file from gVCF files.
minimal
Minimal is a Jekyll theme for GitHub Pages
mkbigfifo
A script to make FIFO files (pipes) with the maximum allowed buffer size
nanopore-sv
A pipeline for Oxford nanopore ont structural variant calling
ngs-performance-choices
Which tools to choose based on various performance metrics.
pacbio-subreads-processing
A Workflow for preprocessing PacBio reads. Category: Multi-Sample InDevelopment
pacbio-variantcalling
Variant calling workflow for targetted PacBio read data. Category:Multi-Sample
pipeline-template
A pipeline template for modular pipelines
prepull-singularity
A tool for pulling singularity images in HPC environments.
qc
A BioWDL workflow for gathering QC metrics on and prepocessing FASTQ files. Category:Single-Sample
reassembly
Maps reads back to an assembly, extracts mapped reads, and starts a new assembly.
rna-coding-potential
This pipeline checks the coding potential of a RNA molecule with several tools.
rna-seq
A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample
scripts
Scripts for releasing, updating docs etc. in biowdl repos
sequence-classification
A workflow for processing metagenomics data sets using Centrifuge. Category:Single-Sample
singularity-permanent-cache
Creates a permanent cache for singularity images on disk.
small-rna
Small rna pipeline. Category:Multi-Sample
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