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analysis_pipeline_cwl

CWL for running analysis pipeline scripts as workflows

aofarrel

bam-to-cram-wdl

A classic.

checker-wdl-templates

Templates for checker WDLs.

clockwork-wdl

WDLization of clockwork

covstats-wdl

WDLized version of covstats from goleft. Get coverage, read length, and more from bam or cram files.

create_contaminated_samples

Simulate cross-sample-contamination by mixing fastq reads from two samples

cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

cwl_wdl_comparomatic-public-

decon

Decon-taminate your Mycobacterium tuberculosis complex fastqs

diffdiff

Highlight the differences between genomic diff files by "aligning" them by position

dockstore-dictionary

An unofficial dictionary for Dockstore.

dockstore-documentation

The documentation for Dockstore.org

dockstore-ui2

Website user interface for Dockstore in Angular2

dockstore-workflow-md5sum-unified

bug testing. this fork will probably be deleted at some point.

documentation

A place for tutorials and other documentation for DataSTAGE platforms

dogpound

Never, ever do this

enabrowsertools-wdl

WDLization of some of enaBrowserTools

fairyland

Test repository. Contents subject to change without notice!

fastp-wdl

WDLization of fastp.

fastqc-wdl

fastqc, but in WDL

fetch_gs_frm_json

Really basic script to parse a json and download the gs:// schemas for google bucket files within.

fragpipe-proteomics-pipeline-tutorial

CWL descriptions for FragPipe Proteomics Pipline

fresh-foo

A fresh repository full of foo.

gatk

Official code repository for GATK versions 4 and up

gatk4-data-processing

Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools

gitflow

HubFlow: A Git extension to make it easy to use GitFlow with GitHub. Based on the original gitflow extension for git.

glossarpy

Create a plaintext or RST glossary using Python

goleft-wdl

Collection of miscellanous WDLized goleft functions.

gs-plugin

Dockstore Google Cloud Storage file provisioning plugin