DKFZ - ODCF's repositories
ACEseqWorkflow
Allele-specific copy number estimation with whole genome sequencing
AlignmentAndQCWorkflows
The DKFZ alignment workflow plugin originally developed at the eilslabs
SNVCallingWorkflow
The DKFZ-ODCF, formerly DKFZ/eilslabs SNV-Calling Workflow
IndelCallingWorkflow
A Platypus-based workflow for indel calling
RNAseqWorkflow
Roddy RNA-seq Workflow Plugin
ldap-summary
Simple shellscripts to make interaction with LDAP/AD/ldapsearch easier
methylCtools-fingerprint
Fingerprinting code originally part of the the methylCtools of Volker Hovestadt.
nf-bam2fastq
Nextflow-based BAM-to-FASTQ conversion and FASTQ-sorting workflow.
SophiaWorkflow
A Roddy plugin to run the Sophia tool.
COWorkflowsBasePlugin
A basic Roddy plugin for computational oncology workflows
ega-cluster-cryptor
parallelise encryption of EGA submissions onto a cluster - a partial EgaCryptor replacement
ega-xml-dl
batch download everything in your EGA or ENA submission account
example-cwlexec-singularity
An example CWL workflow to be run with Singularity on an LSF cluster
igv-crawler
Crawl any filesystem for genome data, providing one-click opening in IGV. READ ONLY REPOSITORY.
odcf-guide
Read-Only mirror; please see GitLab for main repo
bioinformatic-reproducibility-course
A course on basic tools for reproducibility in bioinformatics
FastqIndEx
A tool to index and extract data from gzipped FASTQ files
reference-data
Code to setup and maintain reference assemblies and accompanying data
COWorkflows
Legacy repository for the COWorkflows plugin
FastqIndEx-integration-testing
Test script(s) to perform integration tests for the FastqIndEx'er
methylCtools
analysis of whole-genome bisulfite sequencing data
setup-reference-data
Code and documentation for setting up reference data for the DKFZ-ODCF workflows, including reference genomes and their supplementary files, annotation data, etc.
snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see