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aligning

A collection of BioWDL workflows for aligning sequencing data.

all-pipelines

Contains all biowdl pipelines for maintenance purposes

ansible-cromwell-database

Sets up a cromwell database server.

bam-to-gvcf

A BioWDL workflow for generating gVCF files from BAM files.

bammetrics

A BioWDL workflow for gathering metrics from a BAM file. Category:Single-Sample

biotdg

Bioinformatics Test Data Generator

biowdl-docs-theme

A theme for the BioWDL docs.

biowdl-input-converter

Converts sample configuration files into WDL structs in JSON format.

biowdl-test-data

Reproducible and reusable test data for bioinformatics projects.

biowdl.github.io

The BioWDL organisation github.io site.

chip-seq

A BioWDL pipeline for processing ChIP-seq data.

chunked-scatter

clinical-validation

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

cnv-calling

Biowdl pipelines for CNV calling. Working from indexed bam files.

collect-columns

compare-gff

A pipeline to compare a General Feature Format file to other General Feature Format 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-cromwell-database

A docker container containing a database for cromwell.

docker-cuppa

A docker image for hartwigmedical/hmftools' CUPPA.

docker-curl

A debian container with curl installed.

docker-gridss

docker-health-checker

A docker image containing the Hartwig Medical Foundation's health-checker

docker-linx

A docker image containing the Hartwig Medical Foundation's linx.

docker-mergecounts

docker-orange

A docker image for hartwigmedical/hmftools' orange.