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BioWDL (@biowdl)

biowdl

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tasks

A collection of reusable WDL tasks. Category:Other

RNA-seq

A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample

germline-DNA

A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample

wdl-aid

Automatic Input Documentation for WDL workflows

wdl-packager

Package a WDL and its imports into a zip file

structural-variantcalling

A workflow for calling structural variants. Category:Single-Sample

somatic-variantcalling

A pipeline for somatic variantcalling. Category:Single-Sample

WGSinCancerDiagnostics

ngs-performance-choices

Which tools to choose based on various performance metrics.

mkbigfifo

A script to make FIFO files (pipes) with the maximum allowed buffer size

prepull-singularity

A tool for pulling singularity images in HPC environments.

pipeline-template

A pipeline template for modular pipelines

biowdl-test-data

Reproducible and reusable test data for bioinformatics projects.

gatk-variantcalling

A pipeline that calls variants on a group of BAM files. Category:Multi-Sample

singularity-permanent-cache

Creates a permanent cache for singularity images on disk.

QC

A BioWDL workflow for gathering QC metrics on and prepocessing FASTQ files. Category:Single-Sample

gatk-preprocess

A BioWDL workflow for preprocessing BAM files for variantcalling. Based on the GATK Best Practices. Category:Single-Sample

collect-columns

scripts

Scripts for releasing, updating docs etc. in biowdl repos

expression-quantification

A BioWDL workflow for quantifying expression. Category:Multi-Sample

TALON-WDL

WDL implementation of the TALON workflow. Category:Multi-Sample InDevelopment

uniparental-disomy

A simple pipeline to find uniparental-disomy based on GVCF data using UPDio

compare-gff

A pipeline to compare a General Feature Format file to other General Feature Format files.

biotdg

Bioinformatics Test Data Generator

clinical-validation

Check if a VCF for a benchmark sample matches the given output.

ansible-cromwell-database

Sets up a cromwell database server.

bam-to-gvcf

A BioWDL workflow for generating gVCF files from BAM files.

virus-assembly

A BioWDL pipeline for virus assembly.

biowdl.github.io

The BioWDL organisation github.io site.

sequence-classification

A workflow for processing metagenomics data sets using Centrifuge. Category:Single-Sample