Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

Package Usage: actions: snakemake/snakemake-github-action

Run Snakemake on the repository
36 versions
Latest release: 10 months ago

View more package details: https://packages.ecosyste.ms/registries/github%20actions/packages/snakemake/snakemake-github-action

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Dependent Repos 121

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.
  • v1.22.0 .github/workflows/benchmark-giab.yml
  • v1.24.0 .github/workflows/main.yml
  • v1 .github/workflows/main.yml

Size: 17.5 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

SchlossLab/mikropml-snakemake-workflow
Snakemake template for building reusable and scalable machine learning pipelines with mikropml
  • v1.24.0 .github/workflows/build.yml
  • v1 .github/workflows/build.yml
  • v1.24.0 .github/workflows/run-snakemake.yml
  • v1.24.0 .github/workflows/tests.yml

Size: 6.75 MB - Last synced: 30 days ago - Pushed: 10 months ago

tahiri-lab/aPhyloGeo-pipeline
Phylogeographic workflow using sliding-windows, RAxML-NG and FastTree
  • v1.24.0 .github/workflows/main.yml

Size: 3.39 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

IKIM-Essen/uncovar
Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.
  • v1.24.0 .github/workflows/main.yml
  • v1.24.0 .github/workflows/release-please.yml

Size: 3.83 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

visze/sequence_cnn_models
  • v1.24.0 .github/workflows/main.yml

Size: 1.54 MB - Last synced: 4 months ago - Pushed: 4 months ago

T3choH4ck3r/array
  • v1.22.0 .github/workflows/main.yml

Size: 14.7 MB - Last synced: about 2 months ago - Pushed: over 2 years ago

Zilong-Li/lcWGS-imputation-workflow
Imputation workflow for low coverage whole genome sequencing data
  • v1.24.0 .github/workflows/main.yml

Size: 198 KB - Last synced: about 1 month ago - Pushed: about 1 month ago

kikkomep/test-nfcore-template
  • v1.24.0 .github/workflows/main.yml

Size: 2.19 MB - Last synced: over 1 year ago - Pushed: over 1 year ago

alhenry/cvd1-hf
Analysis code for Olink CVD1 - HF analysis
  • v1.5.3 .github/workflows/main.yaml

Size: 22.7 MB - Last synced: 7 months ago - Pushed: over 1 year ago

koesterlab/rna-seq-kallisto-sleuth Fork of snakemake-workflows/rna-seq-kallisto-sleuth
  • v1.14.0 .github/workflows/main.yml
  • v1.6.0 .github/workflows/main.yml

Size: 5.41 MB - Last synced: 10 months ago - Pushed: 10 months ago

konnorve/Variant-finding-workflow
  • v1.5.3 .github/workflows/main.yaml

Size: 2.8 MB - Last synced: about 2 months ago - Pushed: about 1 year ago

snakemake-workflows/dna-seq-neoantigen-prediction
Snakemake workflow for neoantigen prediction
  • v1.17.0 .github/workflows/main.yaml

Size: 34.3 MB - Last synced: 9 months ago - Pushed: 9 months ago

ebi-gene-expression-group/bulk-recalculations
Snakemake workflow for new experiments processing, reprocessing and recalculations steps
  • v1 .github/workflows/pr.yaml

Size: 556 KB - Last synced: about 2 months ago - Pushed: 3 months ago

Xavster838/coreDupGraph
  • v1.22.0 .github/workflows/lint.yml
  • v1.22.0 .github/workflows/main.yml

Size: 219 KB - Last synced: 6 months ago - Pushed: 6 months ago

MaNyh/NTRFlows
  • v1.24.0 .github/workflows/main.yml

Size: 16.2 MB - Last synced: 10 months ago - Pushed: over 1 year ago

esbenlykke/drought_index
A project to practice reproducible research practices while studiyng the state of drought around the world.
  • v1 .github/workflows/run_pipeline.yml

Size: 124 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

kilpert/dna-seq-varlociraptor Fork of snakemake-workflows/dna-seq-varlociraptor
Variant detection with Delly and Freebayes, followed by statistical assessment with Varlociraptor
  • v1.24.0 .github/workflows/main.yml
  • v1 .github/workflows/main.yml
  • v1.22.0 .github/workflows/benchmark-giab.yml

Size: 19.6 MB - Last synced: 9 months ago - Pushed: 9 months ago

WEHIGenomicsRnD/qc-pipe
Multi-purpose pipeline for generating QC metrics from sequencing data
  • v1.22.0 .github/workflows/main.yml
  • v1.23.0 .github/workflows/main.yml

Size: 55.8 MB - Last synced: 3 months ago - Pushed: 12 months ago

sanjaynagi/AmpSeeker
A state-of-the-art snakemake workflow for amplicon sequencing
  • v1.23.0 .github/workflows/github-action-ampseq.yml

Size: 77.6 MB - Last synced: 11 days ago - Pushed: 11 days ago

bionumpy/bionumpy Fork of knutdrand/bionumpy
Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/
  • v1 .github/workflows/benchmarking.yml
  • v1 .github/workflows/benchmarking_big.yml
  • v1 .github/workflows/manuscript.yml

Size: 36.4 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

dbespiatykh/TBvar
Variant detection and lineage barcoding of Mycobacterium tuberculosis
  • v1.23.0 .github/workflows/main.yml

Size: 128 MB - Last synced: 7 months ago - Pushed: about 1 year ago

hydra-genetics/misc
  • v1.22.0 .github/workflows/lint.yaml

Size: 176 KB - Last synced: 2 days ago - Pushed: 2 days ago

NBChub/snakemake-UmetaFlow
Created for testing the metabolomics pipeline through snakemake
  • v1.24.0 .github/workflows/push.yaml

Size: 622 MB - Last synced: 21 days ago - Pushed: about 1 year ago

snakemake-workflows/rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
  • v1.22.0 .github/workflows/main.yml

Size: 16.5 MB - Last synced: 2 months ago - Pushed: 2 months ago

pommevilla/drought_index
  • v1 .github/workflows/run_pipeline.yml

Size: 168 MB - Last synced: 9 days ago - Pushed: 9 days ago

armossa/Drought_index
Practice reproducible research while studying the state of drought around the globe
  • v1 .github/workflows/run_pipeline.yml

Size: 65.5 MB - Last synced: 5 months ago - Pushed: 5 months ago

Dartmouth-Data-Analytics-Core/DAC-RNAseq-pipeline
Pipeline for processing and quality control of RNA-seq data
  • v1 .github/workflows/test.yml

Size: 30.7 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

dodslaser/cnv_sv Fork of hydra-genetics/cnv_sv
Collection of rules used to call structural variants
  • v1.22.0 .github/workflows/lint.yaml

Size: 23.1 MB - Last synced: 9 months ago - Pushed: over 1 year ago

NBISweden/aMeta
Ancient microbiome snakemake workflow
  • v1.24.0 .github/workflows/main.yaml

Size: 9.61 MB - Last synced: 18 days ago - Pushed: 19 days ago

CVUA-RRW/FooDMe
A reproducible and scalable snakemake workflow for the analysis of DNA metabarcoding experiments, with a special focus on food and feed samples.
  • v1.24.0 .github/workflows/integration.yaml
  • v1.23.0 .github/workflows/integration.yaml
  • v1.23.0 .github/workflows/linter.yaml

Size: 3.88 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

LeandroRitter/aMeta Fork of NBISweden/aMeta
Ancient microbiome snakemake workflow
  • v1.24.0 .github/workflows/main.yaml

Size: 9.75 MB - Last synced: 10 days ago - Pushed: 10 days ago

quevedor2/rna-seq-star-deseq2 Fork of snakemake-workflows/rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
  • v1.14.0 .github/workflows/main.yml
  • v1.6.0 .github/workflows/main.yml

Size: 16.6 MB - Last synced: 4 months ago - Pushed: 4 months ago

SichongP/atac-seq
Snakemake workflow for ATAC-seq analysis
  • v1.24.0 .github/workflows/main.yml

Size: 193 KB - Last synced: about 1 month ago - Pushed: over 1 year ago

percyfal/tswf
Whole genome tree sequence analyses
  • v1.24.0 .github/workflows/main.yaml

Size: 3 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

AU-ENVS-Bioinformatics/IlluminaSnakemake
A pipeline for processing raw Illumina reads to draft assemblies and annotations.
  • v1.24.0 .github/workflows/main.yml

Size: 118 KB - Last synced: about 1 year ago - Pushed: about 1 year ago

supermaxiste/ARPEGGIO
A SnakeMake workflow to analyse whole genome bisulfite sequencing data from allopolyploids.
  • v1 .github/workflows/main.yml

Size: 84.3 MB - Last synced: 3 months ago - Pushed: 10 months ago

IKIM-Essen/RiboSnake
16S pipeline using qiime2 created with snakemake
  • v1 .github/workflows/main.yaml

Size: 97.5 MB - Last synced: 10 days ago - Pushed: 10 days ago

snakemake-workflows/rna-seq-kallisto-sleuth
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
  • v1.22.0 .github/workflows/main.yml
  • v1.23.0 .github/workflows/main.yml

Size: 5.39 MB - Last synced: 10 days ago - Pushed: 10 days ago

zifornd/shrnaseq
  • v1.24.0 .github/workflows/main.yml

Size: 446 MB - Last synced: 2 months ago - Pushed: about 1 year ago

seankmartin/atn-sub-lfp-workflow
Working with snakemake for analysis of SUB LFP
  • v1.24.0 .github/workflows/main.yml

Size: 18 MB - Last synced: about 2 months ago - Pushed: 6 months ago

one-datum/pipeline
What can we infer about an orbit from just the RV jitter?
  • v1.24 .github/workflows/pipeline.yaml

Size: 3.09 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

johnne/map_metaT
Snakemake workflow to map and quantify metatranscriptomic data using a metagenome reference
  • v1.24.0 .github/workflows/main.yml

Size: 49.8 KB - Last synced: 11 months ago - Pushed: 11 months ago

vdclab/sORTholog
  • v1.22.0 .github/workflows/test.yaml

Size: 17.2 MB - Last synced: 3 months ago - Pushed: 3 months ago

snakemake-workflows/dna-seq-benchmark
A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets
  • v1.24.0 .github/workflows/main.yml

Size: 170 KB - Last synced: about 2 months ago - Pushed: about 2 months ago

kokyriakidis/dna-seq-varlociraptor Fork of 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.
  • v1.24.0 .github/workflows/main.yml

Size: 52.1 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

visze/MPRAsnakeflow Fork of kircherlab/MPRAsnakeflow
new implementation of MPRAsnakeflow fork of MPRAflow
  • v1.24.0 .github/workflows/main.yml

Size: 41.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

guillaumecharbonnier/mw-lib
Metaworkflow library of generalised Snakemake rules
  • v1.13.0 .github/workflows/tests.yml

Size: 892 KB - Last synced: 2 months ago - Pushed: 2 months ago

kircherlab/MPRAsnakeflow
new implementation of MPRAsnakeflow fork of MPRAflow
  • v1.24.0 .github/workflows/main.yml

Size: 41.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

simonmoulds/gwm-analysis
  • v1.24.0 .github/workflows/main.yml

Size: 513 KB - Last synced: about 1 year ago - Pushed: about 1 year ago

robinmeyers/rna-seq-star-deseq2 Fork of snakemake-workflows/rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
  • v1.22.0 .github/workflows/main.yml

Size: 16.6 MB - Last synced: 5 months ago - Pushed: 5 months ago

friendsofstrandseq/mosaicatcher-pipeline
Integrated workflow for SV calling from single-cell Strand-seq data
  • v1.24.0 .github/workflows/conda.yaml
  • v1.24.0 .github/workflows/main.yaml

Size: 848 MB - Last synced: 4 months ago - Pushed: 4 months ago

snakemake-workflows/dna-seq-mtb
A flavor of https://github.com/snakemake-workflows/dna-seq-varlociraptor preconfigured for molecular tumor boards
  • v1.24.0 .github/workflows/main.yml

Size: 2.92 MB - Last synced: 16 days ago - Pushed: 17 days ago

dbespiatykh/RDscan
A snakemake workflow for regions of difference discovery in Mycobacterium tuberculosis complex (MTBC) samples
  • v1.23.0 .github/workflows/main.yml

Size: 79.4 MB - Last synced: 4 months ago - Pushed: 4 months ago

Tuks-ICMM/Pharmacogenetic-Analysis-Pipeline
A Snakemake powered pipeline developed to perform variant-effect-prediction and frequency analysis given multiple Variant Call Format datasets. This has been developed in partial fulfilment of a MSc in Bioinformatics at the University of Pretoria by Graeme Ford.
  • v1.23.0 .github/workflows/snakemake-tests.yml

Size: 65.7 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

NBISweden/LTS-BiodiversityAnalysisCAO
Code repository for the support project P_Snoeijs-Leijonmalm_2205
  • v1 .github/workflows/main.yml

Size: 2.4 MB - Last synced: 7 months ago - Pushed: 7 months ago

hdr-bgnn/BGNN_Core_Workflow
First complet version of the workflow with snakemake
  • v1.23.0 .github/workflows/snakemake-lint.yml

Size: 8.82 MB - Last synced: 6 months ago - Pushed: 6 months ago

hydra-genetics/sentieon
  • v1.24.0 .github/workflows/lint.yaml

Size: 116 KB - Last synced: 3 months ago - Pushed: 3 months ago

Ovewh/Climaso
The CLimate IMpact of AeroSOls: forcing and feedbacks
  • v1.24.0 .github/workflows/main.yml

Size: 7.66 MB - Last synced: about 12 hours ago - Pushed: about 13 hours ago

harvardinformatics/snpArcher
Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
  • v1.24.0 .github/workflows/main.yaml

Size: 128 MB - Last synced: 15 days ago - Pushed: 16 days ago

daltonkw/drought_index
A project to practice reproducible practices -> Riffomas
  • v1 .github/workflows/run_pipeline.yml

Size: 229 MB - Last synced: 5 months ago - Pushed: 5 months ago

arendscm/dna-seq-gatk-variant-calling Fork of snakemake-workflows/dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow
  • v1.17.0 .github/workflows/main.yml

Size: 9.15 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

EichlerLab/ONT_pipelines
  • v1.23.0 .github/workflows/lint.yml
  • v1.23.0 .github/workflows/main.yml

Size: 161 MB - Last synced: 20 days ago - Pushed: 4 months ago

cbg-ethz/V-pipe
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
  • v1.19.0 .github/workflows/run_regression_tests.yaml

Size: 14.8 MB - Last synced: about 8 hours ago - Pushed: about 9 hours ago

simonmoulds/uk-decadal-flood-prediction
  • v1.24.0 .github/workflows/main.yml

Size: 3.35 MB - Last synced: 11 months ago - Pushed: over 1 year ago

ocisse/dna-seq-gatk-variant-calling
  • v1.7.0 .github/workflows/main.yml

Size: 7.93 MB - Last synced: 10 months ago - Pushed: over 3 years ago

ivargr/hierarchical_results
Simple test of a hierarchical disk-backed logger
  • v1 .github/workflows/manuscript.yml.disabled

Size: 50.8 KB - Last synced: 27 days ago - Pushed: about 1 year ago

isaacvock/fastq2bakR
Extension of rna-seq-star-deseq2 Snakemake workflow to process NR-seq data for bakR
  • v1.22.0 .github/workflows/main.yml

Size: 7.13 MB - Last synced: 10 months ago - Pushed: about 1 year ago

kircherlab/MPRAOligoDesign
Basic scripts for creating an oligo design file
  • v1.24.0 .github/workflows/main.yml

Size: 117 MB - Last synced: 6 months ago - Pushed: 6 months ago

zhujack/dna-seq-gatk-variant-calling
test
  • master .github/workflows/main.yml

Size: 1.23 MB - Last synced: over 1 year ago - Pushed: about 4 years ago

simonmoulds/decadal-prediction-data-preparation
  • v1.24.0 .github/workflows/main.yml

Size: 110 KB - Last synced: over 1 year ago - Pushed: over 1 year ago

simonmoulds/aquacrop-vegmon-analysis
Constraining a crop model with smartphone imagery collected by citizen scientists
  • v1.24.0 .github/workflows/main.yml

Size: 1.95 KB - Last synced: over 1 year ago - Pushed: over 1 year ago

simonmoulds/us-streamflow-prediction
Experiments on deep learning for streamflow prediction in the US
  • v1.24.0 .github/workflows/main.yml

Size: 21.5 KB - Last synced: 12 months ago - Pushed: 12 months ago

simonmoulds/jules-mosart
  • v1.24.0 .github/workflows/main.yml

Size: 69.3 KB - Last synced: over 1 year ago - Pushed: over 1 year ago

simonmoulds/jules-ganges-data-preparation
  • v1.24.0 .github/workflows/main.yml

Size: 59.6 KB - Last synced: over 1 year ago - Pushed: over 1 year ago

visze/new_project
test snakemake workflow
  • v1.5.3 .github/workflows/main.yaml

Size: 58.6 KB - Last synced: over 1 year ago - Pushed: over 3 years ago

gitbackspacer/rna-seq-kallisto-sleuth-test
  • v1.6.0 .github/workflows/main.yml

Size: 42 KB - Last synced: over 1 year ago - Pushed: over 3 years ago

whtns/dna-seq-varlociraptor
  • v1.9.0 .github/workflows/main.yml

Size: 229 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago

Xavster838/run_NucFreq
  • v1.22.0 .github/workflows/lint.yml
  • v1.22.0 .github/workflows/main.yml

Size: 86.9 KB - Last synced: about 1 year ago - Pushed: about 2 years ago

DessimozLab/fold_tree
snakemake pipeline for creating trees from sequence sets
  • v1.24.0 .github/workflows/main.yml

Size: 205 MB - Last synced: 6 months ago - Pushed: 6 months ago

koesterlab/ngs-fastq-to-cram
Snakemake workflow for converting FASTQ files to self-contained CRAM files with maximum lossless compression.
  • v1.24.0 .github/workflows/main.yml

Size: 1000 Bytes - Last synced: over 1 year ago - Pushed: over 2 years ago