DKFZ-ODCF repositories

26 repositories

COWorkflowsBasePlugin
Public
A basic Roddy plugin for computational oncology workflows
ngs roddy
ngs roddy
Groovy
•
MIT License
•2•2•10•0•Updated Jul 13, 2026Jul 13, 2026
AlignmentAndQCWorkflows
Public
The DKFZ alignment workflow plugin originally developed at the eilslabs
workflow bam-files quality-control
workflow bam-files quality-control alignment wes wgbs bwa bwa-mem conda-environment fastq-files
Python
•
Other
•5•7•47•2•Updated Jul 8, 2026Jul 8, 2026
SNVCallingWorkflow
Public
The DKFZ-ODCF, formerly DKFZ/eilslabs SNV-Calling Workflow
workflow snp variant-calling
workflow snp variant-calling variant-annotation roddy
Python
•
Other
•4•10•2•2•Updated Dec 4, 2025Dec 4, 2025
sophia
Public
The Sophia structural variation caller. Fork of https://bitbucket.org/utoprak/sophia.
C++
•
GNU General Public License v3.0
•0•3•14•2•Updated Jul 25, 2025Jul 25, 2025
igv-crawler
Public
Crawl any filesystem for genome data, providing one-click opening in IGV. READ ONLY REPOSITORY.
visualization crawler bioinformatics
visualization crawler bioinformatics genomics perl perl5 igv
Perl
•
MIT License
•1•2•1•0•Updated Sep 24, 2024Sep 24, 2024
SophiaWorkflow
Public
A Roddy plugin to run the Sophia tool.
Python
•
GNU General Public License v2.0
•1•7•6•0•Updated Jul 30, 2024Jul 30, 2024
IndelCallingWorkflow
Public
A Platypus-based workflow for indel calling
workflow somatic-variants cancer-genomics
workflow somatic-variants cancer-genomics platypus indels roddy somatic-indels
Python
•
Other
•5•6•4•2•Updated Jul 29, 2024Jul 29, 2024
RNAseqWorkflow
Public
Roddy RNA-seq Workflow Plugin
bioinformatics-pipeline rna rna-seq-pipeline
bioinformatics-pipeline rna rna-seq-pipeline roddy
Perl
•4•9•7•0•Updated Jun 12, 2024Jun 12, 2024
nf-bam2fastq
Public
Nextflow-based BAM-to-FASTQ conversion and FASTQ-sorting workflow.
docker workflow sorting
docker workflow sorting bam-files nextflow conversion conda singularity fastq fastq-files
Shell
•4•4•9•1•Updated Mar 8, 2024Mar 8, 2024
odcf-guide
Public
Read-Only mirror; please see GitLab for main repo
Kotlin
•
Other
•0•2•0•0•Updated Jan 25, 2024Jan 25, 2024
ACEseqWorkflow
Public
Allele-specific copy number estimation with whole genome sequencing
workflow genome-sequencing copy-number-variation
workflow genome-sequencing copy-number-variation structural-variation gc-correction roddy
R
•
MIT License
•10•23•2•1•Updated Nov 10, 2023Nov 10, 2023
methylCtools
Public
analysis of whole-genome bisulfite sequencing data
Python
•
MIT License
•3•0•0•0•Updated Jun 27, 2023Jun 27, 2023
nf-arriba
Public
Nextflow
•
MIT License
•0•0•0•0•Updated Feb 24, 2023Feb 24, 2023
COWorkflows
Public
Legacy repository for the COWorkflows plugin
Perl
•0•0•0•0•Updated Sep 29, 2022Sep 29, 2022
methylCtools-fingerprint
Public
Fingerprinting code originally part of the the methylCtools of Volker Hovestadt.
R
•1•3•0•0•Updated Feb 15, 2022Feb 15, 2022
bioinformatic-reproducibility-course
Public
A course on basic tools for reproducibility in bioinformatics
Other
•1•0•0•0•Updated Dec 9, 2021Dec 9, 2021
FastqIndEx-integration-testing
Public
Test script(s) to perform integration tests for the FastqIndEx'er
gzip fastq fastqindex
gzip fastq fastqindex
Groovy
•
MIT License
•1•0•0•0•Updated Dec 9, 2021Dec 9, 2021
setup-reference-data
Public archive
Code and documentation for setting up reference data for the DKFZ-ODCF workflows, including reference genomes and their supplementary files, annotation data, et…
Shell
•
MIT License
•1•0•0•0•Updated Dec 9, 2021Dec 9, 2021
ldap-summary
Public
Simple shellscripts to make interaction with LDAP/AD/ldapsearch easier
bash cli ldap
bash cli ldap active-directory
Shell
•
MIT License
•2•5•0•0•Updated Dec 9, 2021Dec 9, 2021
ega-xml-dl
Public
batch download everything in your EGA or ENA submission account
downloader xml bash-script
downloader xml bash-script ega-archive
Python
•
MIT License
•1•1•1•0•Updated Dec 9, 2021Dec 9, 2021
ega-cluster-cryptor
Public
parallelise encryption of EGA submissions onto a cluster - a partial EgaCryptor replacement
lsf bash-script lsf-jobs
lsf bash-script lsf-jobs cluster-computing pbs encryption-utility ega-archive
Shell
•
MIT License
•2•2•1•0•Updated Dec 9, 2021Dec 9, 2021
example-cwlexec-singularity
Public
An example CWL workflow to be run with Singularity on an LSF cluster
Common Workflow Language
•
MIT License
•1•1•0•0•Updated Dec 9, 2021Dec 9, 2021
FastqIndEx
Public
A tool to index and extract data from gzipped FASTQ files
stream gzip zlib
stream gzip zlib ngs extraction indexing index fastq random-access reads
C++
•
MIT License
•1•2•18•1•Updated Dec 9, 2021Dec 9, 2021
reference-data
Public
Code to setup and maintain reference assemblies and accompanying data
Shell
•1•0•10•0•Updated Dec 9, 2021Dec 9, 2021
snakemake-wrappers
Public
This is the development home of the Snakemake wrapper repository, see
Python
•215•0•0•0•Updated Dec 9, 2021Dec 9, 2021
DKFZBiasFilter
Public
Python
•
GNU General Public License v3.0
•7•12•2•2•Updated Dec 8, 2021Dec 8, 2021

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DKFZ - ODCF

All

26 repositories

COWorkflowsBasePlugin

AlignmentAndQCWorkflows

SNVCallingWorkflow

sophia

igv-crawler

SophiaWorkflow

IndelCallingWorkflow

RNAseqWorkflow

nf-bam2fastq

odcf-guide

ACEseqWorkflow

methylCtools

nf-arriba

COWorkflows

methylCtools-fingerprint

bioinformatic-reproducibility-course

FastqIndEx-integration-testing

setup-reference-data

ldap-summary

ega-xml-dl

ega-cluster-cryptor

example-cwlexec-singularity

FastqIndEx

reference-data

snakemake-wrappers

DKFZBiasFilter

Repositories list

26 repositories