common-workflow-language/common-workflow-language

Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

Language: Common Workflow Language - Size: 3.63 MB - Last synced at: 2 days ago - Pushed at: 6 months ago - Stars: 1,466 - Forks: 195

common-workflow-language/cwltool

Common Workflow Language reference implementation

Language: Python - Size: 11.3 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 348 - Forks: 232

snakemake-workflows/rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

Language: Python - Size: 16.6 MB - Last synced at: 2 months ago - Pushed at: 10 months ago - Stars: 339 - Forks: 208

snakemake-workflows/dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow

Language: Python - Size: 9.14 MB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 250 - Forks: 145

snakemake-workflows/dna-seq-varlociraptor

A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.

Language: Python - Size: 17.7 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 86 - Forks: 42

snakemake-workflows/rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

Language: Python - Size: 5.75 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 68 - Forks: 45

akcorut/kGWASflow

kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.

Language: Python - Size: 610 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 24 - Forks: 5

nodrogluap/tamor

Illumina Dragen cancer genome and transcriptome analysis automation using Snakemake

Language: Python - Size: 381 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 7 - Forks: 1

fairagro/m4.4_sciwin_client

🦀 SciWIn Client: Reproducible computational Workflows made easy!

Language: Rust - Size: 1.95 MB - Last synced at: about 19 hours ago - Pushed at: about 21 hours ago - Stars: 5 - Forks: 1

tomarovsky/BuscoClade

Snakemake pipeline to construct species phylogenies using BUSCOs

Language: Python - Size: 416 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 4 - Forks: 2

nikostr/dna-seq-deepvariant-glnexus-variant-calling

A Snakemake workflow for variant calling with DeepVariant, and optionally joint variant calling using GLnexus.

Language: Python - Size: 86.1 MB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 4 - Forks: 1

tucca-cellag/tucca-rna-seq

[UNDER-CONSTRUCTION] TUCCA's RNA-Seq Workflow for Cellular Agriculture Projects

Language: Python - Size: 25.9 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 1 - Forks: 0

kinow/wrf-sandbox

Size: 5.86 KB - Last synced at: about 2 months ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0