All standardized workflows

All workflows according to ‘standardized usage’

Workflow	Description	Topics	Reporting	Stars	Watchers
snakemake-workflows/rna-seq-star-deseq2	RNA-seq workflow using STAR and DESeq2	snakemake sciworkflows reproducibility gene-expression-analysis deseq2	last update 2024-09-13formatting: passedlinting: passed	321	11
snakemake-workflows/dna-seq-gatk-variant-calling	This Snakemake pipeline implements the GATK best-practices workflow	reproducibility snakemake sciworkflows genomic-variant-calling gatk	last update 2023-06-29formatting: failedlinting: passed	207	9
franciscozorrilla/metaGEM	:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and pred…	metagenomics computational-biology metabolic-models gut-microbiome snakemake metagenome-assembled-genomes mags metabolism bioinformatics flux-balance-analysis genome-scale-metabolic-model metabolic-modeling microbial-ecology microbiome systems-biology	last update 2024-09-19formatting: failedlinting: failed	189	5
cbg-ethz/V-pipe	V-pipe is a pipeline designed for analysing NGS data of short viral genomes	ngs snakemake conda biohackeu20 virus sequencing bioinformatics bioinformatics-pipeline biohackcovid20 sars-cov-2 sarscov2 hiv genomics biohackeu21 biohackeu22	last update 2025-01-24formatting: passedlinting: failed	134	11
moiexpositoalonsolab/grenepipe	A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads,…	variant-calls snakemake evolve-and-resequence population-genetics ancient-dna variant-calling pool-sequencing genomic-variant-calling snakemake-workflow	last update 2025-02-24formatting: passedlinting: failed	96	4
mrvollger/StainedGlass	Make colorful identity heatmaps of genomic sequence		last update 2024-07-16formatting: passedlinting: passed	93	5
snakemake-workflows/dna-seq-varlociraptor	A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/nor…	varlociraptor sciworkflows snakemake reproducibility genomic-variant-calling	last update 2025-03-09formatting: failedlinting: passed	83	7
GooglingTheCancerGenome/sv-callers	Snakemake-based workflow for detecting structural variants in genomic data	bioinformatics structural-variants sv-calling germline-variants somatic-variants cancer-genomics wgs workflow snakemake hpc-applications	last update 2025-02-14formatting: failedlinting: failed	79	4
snakemake-workflows/rna-seq-kallisto-sleuth	A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.	snakemake kallisto sleuth rna-seq differential-expression sciworkflows reproducibility	last update 2025-03-04formatting: failedlinting: passed	67	4
epigen/atacseq_pipeline	Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Mo…	snakemake atac-seq python bioinformatics workflow ngs pipeline biomedical-data-science bash	last update 2024-12-01formatting: failedlinting: failed	48	3
zavolanlab/zarp	The Zavolab Automated RNA-seq Pipeline	bioinformatics rna-seq snakemake conda docker fair high-throughput pipeline reproducible-research singularity transcriptomics workflow	last update 2024-11-02formatting: passedlinting: failed	35	6
epigen/enrichment_analysis	A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment …	bioinformatics genomic-regions enrichment-analysis atac-seq biomedical-data-science chip-seq gene-set-enrichment gene-sets rna-seq visualization pipeline snakemake workflow motif-enrichment-analysis	last update 2024-12-19formatting: failedlinting: failed	32	2
sneuensc/mapache	mapping pipeline for ancient DNA	adna ancient-dna genomics mapping mapper pipeline workflow snakemake fastq bam	last update 2024-10-28formatting: failedlinting: failed	26	5
akcorut/kGWASflow	kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.	snakemake genomics gwas gwas-pipeline kmers bioinformatics-pipeline ngs sciworkflows bioinformatics conda pipeline association-mapping bioinformatics-tool gwas-tools structural-variation workflow	last update 2024-06-11formatting: failedlinting: failed	26	3
epigen/unsupervised_analysis	A general purpose Snakemake workflow and MrBiomics module to perform unsupervised analyses (dimensio…	data-science high-dimensional-data snakemake workflow unsupervised-learning principal-component-analysis umap pca visualization clustering data-visualization dimensionality-reduction heatmap densmap cluster-analysis cluster-validation clustering-algorithm clustree leiden-algorithm	last update 2025-03-04formatting: failedlinting: failed	24	4
epigen/dea_limma	A Snakemake workflow and MrBiomics module for performing and visualizing differential (expression) a…	atac-seq bioinformatics biomedical-data-science chip-seq differential-expression-analysis limma limma-trend limma-voom rna-seq snakemake visualization volcano-plot workflow scrna-seq statistics r	last update 2025-03-06formatting: failedlinting: failed	24	4
ncherric/Iliad	ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applicati…	automatic genetics genomics-data snakemake workflow bioinformatics fastq genomics modularization cram idat vcf	last update 2024-01-21formatting: failedlinting: failed	23	1
IKIM-Essen/uncovar	Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reportin…	sars-cov-2 variant-calling lineage-assignment	last update 2024-11-07formatting: passedlinting: passed	21	3
friendsofstrandseq/mosaicatcher-pipeline	Integrated workflow for SV calling from single-cell Strand-seq data	bioinformatics pipeline snakemake strand-seq mosaicatcher genomics	last update 2024-07-30formatting: failedlinting: failed	21	12
snakemake-workflows/snakemake-workflow-template	A template for standard compliant snakemake-workflows		last update 2022-05-27formatting: failedlinting: passed	20	1
epigen/genome_tracks	A Snakemake workflow and MrBiomics module for easy visualization of genome browser tracks of aligned…	atac-seq bioinformatics pipeline python rna-seq snakemake visualization workflow biomedical-data-science genomic-regions genome-browser genome-track scrna-seq	last update 2024-11-16formatting: failedlinting: failed	19	2
epigen/scrnaseq_processing_seurat	A Snakemake workflow and MrBiomics module for processing and visualizing (multimodal) sc/snRNA-seq d…	bioinformatics workflow snakemake scrna-seq biomedical-data-science cite-seq sccrispr-seq 10xgenomics snrna-seq single-cell visualization	last update 2024-12-18formatting: failedlinting: failed	18	5
epigen/dea_seurat	A Snakemake workflow and MrBiomics module for performing differential expression analyses (DEA) on (…	bioinformatics biomedical-data-science differential-expression-analysis scrna-seq single-cell snakemake snrna-seq visualization workflow volcano-plot	last update 2024-12-03formatting: failedlinting: failed	16	4
epigen/spilterlize_integrate	A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly v…	atac-seq batch-effect chip-seq count-matrix dimensionality-reduction integration ngs normalization rna-seq bioinformatics biomedical-data-science pipeline snakemake visualization workflow confounding-effects	last update 2025-03-04formatting: failedlinting: failed	14	4
epigen/mixscape_seurat	A Snakemake workflow and MrBiomics module for performing perturbation analyses of pooled (multimodal…	bioinformatics biomedical-data-science perturbation-analysis sccrispr-seq scrna-seq single-cell snakemake snrna-seq visualization workflow	last update 2024-11-16formatting: failedlinting: failed	14	4
nismod/open-gira	Open-data Global Infrastructure Risk/Resilience Analysis		last update 2025-02-25formatting: failedlinting: failed	13	4
ncbench/ncbench-workflow	No description available.		last update 2025-01-20formatting: passedlinting: failed	13	5
LiaOb21/colora	A snakemake workflow for de novo genome assembly. It produces chromosome-scale primary/phased assemb…	chromosome-level-assembly genome-assembly genome-scaffolding organelle-assembler	last update 2024-09-18formatting: failedlinting: failed	13	4
SchlossLab/mikropml-snakemake-workflow	Snakemake template for building reusable and scalable machine learning pipelines with mikropml	snakemake machine-learning rstats	last update 2025-02-26formatting: passedlinting: passed	12	7
snakemake-workflows/dna-seq-benchmark	A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM…		last update 2025-02-20formatting: passedlinting: passed	12	1
DavideBrex/SpikeFlow	Pipeline to analyse ChIP-Rx data, i.e ChIP-Seq with reference exogenous genome spike-in normalizatio…	bioinformatics bioinformatics-pipeline chip-seq normalisation snakemake snakemake-workflows spike-ins	last update 2025-02-12formatting: passedlinting: passed	11	1
Zilong-Li/lcWGS-imputation-workflow	Imputation workflow for low coverage whole genome sequencing data	genotype-imputation low-coverage-sequencing snakemake-workflows	last update 2024-08-12formatting: failedlinting: passed	9	3
semenko/serpent-methylation-pipeline	An efficient, documented, reproducible Snakemake methylation analysis pipeline for BS-seq and EM-seq…	bsseq methylation pipeline snakemake emseq bisulfite bs-seq em-seq epigenetics	last update 2025-03-04formatting: failedlinting: failed	8	4
MathiasEskildsen/ONT-AmpSeq	Snakemake workflow to generate OTU tables from barcoded ONT data		last update 2025-01-28formatting: failedlinting: passed	7	2
zavolanlab/mirflowz	Snakemake workflow for the mapping and quantification of miRNAs and isomiRs from miRNA-Seq libraries…	bioinformatics isomirs mirna snakemake workflow	last update 2024-08-19formatting: passedlinting: passed	6	4
usnistgov/defrabb	Genome In A Bottle Development Framework for Assembly Based Benchmarks		last update 2025-03-05formatting: passedlinting: failed	5	1
nodrogluap/tamor	Illumina Dragen cancer genome and transcriptome analysis automation using Snakemake	cancer-genomics dragen mutation-analysis pcgr ruo sciworkflows bioinformatics-pipeline	last update 2025-03-05formatting: failedlinting: failed	5	4
fischuu/Pipeline-Holoruminant-Meta	Easy to use Snakemake metagenomic pipeline that covers a) read-based analysis b) contig based analys…	metagenomics snakemake snakemake-workflow dna metagenome-assembled-genomes	last update 2025-03-09formatting: failedlinting: failed	5	3
zjnolen/PopGLen	Bioinformatics pipeline to process whole genome resequencing data and perform genotype likelihood ba…	snakemake bioinformatics bioinformatics-pipeline genotype-likelihoods population-genomics whole-genome-sequencing museomics angsd	last update 2025-02-11formatting: passedlinting: failed	5	1
IHGGM-Aachen/CNVand	A snakemake workflow to analyse and annotate copy number variants		last update 2024-11-07formatting: failedlinting: passed	5	1
boulardlab/3t-seq	A Snakemake workflow for single copy gene, transposable elements and tRNA expression analysis	bioinformatics-pipeline rna-seq-analysis snakemake transposable-elements trna	last update 2024-11-28formatting: passedlinting: passed	5	1
GooglingTheCancerGenome/sv-gen	Snakemake-based workflow for generating artificial genomes with structural variants	bioinformatics structural-variants cancer-genomics wgs simulator workflow snakemake hpc-applications	last update 2023-01-19formatting: failedlinting: failed	5	4
snakemake-workflows/dna-seq-mtb	A flavor of https://github.com/snakemake-workflows/dna-seq-varlociraptor preconfigured for molecular…		last update 2025-03-06formatting: passedlinting: passed	4	2
kircherlab/MPRAsnakeflow	With this snakemake pipeline you can process your MPRA sequencing data (assignment and count). It is…		last update 2025-02-26formatting: passedlinting: passed	4	2
MPUSP/snakemake-ms-proteomics	Pipeline for automatic processing and quality control of mass spectrometry data	bioinformatics conda mass-spectrometry pipeline proteomics snakemake	last update 2025-01-30formatting: passedlinting: passed	4	1
open2c/distiller-sm	a Snakemake version of distiller - the Open2C Hi-C mapping workflow	bioinformatics bioinformatics-pipeline hi-c hic snakemake snakemake-pipeline snakemake-workflow	last update 2025-01-31formatting: passedlinting: failed	4	8
niekwit/crispr-screens	Snakemake workflow for CRISPR-Cas9 screen analysis	bioinformatics-pipeline crispr-screen-analysis snakemake-workflow	last update 2025-01-31formatting: failedlinting: failed	4	2
MPUSP/snakemake-ont-bacterial-variants	A Snakemake workflow for the identification of variants in bacterial genomes using nanopore long-rea…	bioinformatics-pipeline conda nanopore singularity snakemake variant-calling workflow	last update 2025-01-26formatting: passedlinting: passed	4	2
MPUSP/snakemake-crispr-guides	A Snakemake workflow for the design of small guide RNAs (sgRNAs) for CRISPR applications.	bioinformatics-pipeline crispr crispr-design guide-rna-library python3 r-markdown snakemake workflow	last update 2024-12-16formatting: passedlinting: passed	4	0
niekwit/rna-seq-salmon-deseq2	Snakemake workflow for RNA-Seq differential transcript analysis using Salmon/Deseq2	bioinformatics snakemake snakemake-workflow	last update 2024-09-13formatting: failedlinting: failed	4	1
CVUA-RRW/FooDMe	A reproducible and scalable snakemake workflow for the analysis of DNA metabarcoding experiments, wi…	ngs ngs-pipeline metabarcoding targeted-sequencing snakemake food-monitoring public-health food-authenticity workflow pipeline bioinformatics	last update 2024-09-19formatting: failedlinting: passed	4	2
friendsofstrandseq/ashleys-qc-pipeline	Strand-Seq Quality Control Pipeline based on ashleys-qc	bioinformatics pipeline preprocessing sequencing snakemake strand-seq quality-control genomics	last update 2024-06-18formatting: failedlinting: failed	4	4
tahiri-lab/aPhyloGeo-pipeline	Phylogeographic workflow using sliding-windows, RAxML-NG and FastTree	fasttree neighbor-joining phylogenetics phylogeography raxml robinson-foulds sliding-windows workflow	last update 2023-06-01formatting: failedlinting: passed	4	1
khanlab/SPIMprep	A Snakemake workflow for pre-processing single plane illumination microscopy (SPIM, aka lightsheet m…		last update 2025-02-03formatting: passedlinting: failed	3	2
niekwit/rna-seq-star-tetranscripts	Snakemake workflow for transposable element RNA-Seq using TEtranscripts	ngs-pipeline rna-seq-pipeline snakemake-workflow transposable-elements	last update 2025-02-07formatting: failedlinting: failed	3	1
snakemake-workflows/cyrcular-calling	A Snakemake workflow for ecDNA detection in Nanopore or Illumina sequencing reads derived from DNA s…		last update 2024-10-30formatting: failedlinting: passed	3	2
niekwit/damid-seq	Snakemake workflow for DamID-Seq analysis	bioinformatics-pipeline damid snakemake-workflow	last update 2024-11-22formatting: failedlinting: failed	3	1
niekwit/cut_and_run	Snakemake workflow for Cut & Run	bioinformatics ngs-analysis snakemake snakemake-workflow	last update 2024-06-17formatting: failedlinting: failed	3	1
mrvollger/fastCN-smk	No description available.		last update 2023-02-13formatting: passedlinting: failed	3	2
EichlerLab/ONT_pipelines	No description available.		last update 2024-03-07formatting: failedlinting: failed	3	4
fiberseq/fiberseq-smk	Snakemake pipeline for processing fiberseq data		last update 2023-07-03formatting: failedlinting: failed	3	4
sandragodinhosilva/melange	Melange - Snakemake workflow for genome annotation	genomics snakemake-workflows snakemake workflow	last update 2023-05-17formatting: failedlinting: failed	3	1
dbespiatykh/RDscan	A snakemake workflow for regions of difference discovery in Mycobacterium tuberculosis complex (MTBC…	bioinformatics snakemake mycobacterium mycobacterium-tuberculosis-complex structural-variants bacterial-genome-analysis mycobacterium-tuberculosis	last update 2023-01-26formatting: passedlinting: passed	3	1
clami66/AF_server	No description available.		last update 2023-01-02formatting: failedlinting: failed	3	2
SchlossLab/mothur-snakemake-workflow	Snakemake template for microbial amplicon sequence analysis with mothur.	16s-rrna mothur snakemake	last update 2023-02-09formatting: failedlinting: failed	3	3
StergachisLab/IsoSeq_smk	Pipeline for MAS-Seq processing		last update 2025-03-06formatting: failedlinting: failed	2	5
NCI-CGR/TriosCompass_v2	Trios analysis workflow written in Snakemake		last update 2025-02-19formatting: failedlinting: failed	2	4
MPUSP/snakemake-bacterial-riboseq	Bacterial-Riboseq: A Snakemake workflow for the analysis of riboseq data in bacteria.	bioinformatics-pipeline conda riboseq ribosome-profiling singularity snakemake workflow	last update 2025-02-02formatting: passedlinting: passed	2	1
ChaissonLab/SegDupAnnotation2	Count gene duplications.		last update 2024-11-25formatting: failedlinting: failed	2	4
richardstoeckl/QCforSeqCode	Snakemake Pipeline to check the requirements for a prokaryotic assembly to be included in the SeqCod…		last update 2024-12-05formatting: failedlinting: failed	2	1
Zilong-Li/array-imputation-workflow	imputation workflow for array data using shapeit2 and impute2	genotype-imputation snakemake-workflows snp-array	last update 2024-02-18formatting: failedlinting: failed	2	1
PathoGenOmics-Lab/VIPERA	A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis	bioinformatics intrahost sars-cov-2 virus-evolution reporting snakemake	last update 2024-01-23formatting: failedlinting: failed	2	1
mrvollger/Rhodonite	A workflow for modularly running various repeat masking programs		last update 2022-10-19formatting: failedlinting: failed	2	2
ETH-NEXUS/gExcite_pipeline	single-cell Gene and AnTibody Expression pipeline		last update 2023-05-24formatting: failedlinting: failed	2	7
snakemake-workflows/species-quantification	No description available.		last update 2021-12-20formatting: passedlinting: passed	2	0
ClavelLab/genome-assembly	A Snakemake workflow assembling bacterial genomes according to the standard operating procedure in t…	bacterial-genomes genome-assembly snakemake snakemake-workflows	last update 2025-03-04formatting: failedlinting: failed	1	1
tucca-cellag/tucca-rna-seq	[UNDER-CONSTRUCTION] TUCCA’s RNA-Seq Snakemake Workflow for Cellular Agriculture Projects		last update 2025-03-03formatting: passedlinting: failed	1	1
durr1602/gyoza	Snakemake pipeline to analyze demultiplexed sequencing data of DMS experiment, produce diagnostics p…		last update 2025-02-20formatting: failedlinting: passed	1	1
IKIM-Essen/metagenomics_res	No description available.		last update 2025-02-10formatting: passedlinting: passed	1	1
schlesnerlab/multicondition-deseq2-enrichment	Workflow dervied form https://github.com/snakemake-workflows/rna-seq-star-deseq2 for multi condition…		last update 2025-01-27formatting: passedlinting: failed	1	2
solida-core/dima	Snakemake pipeline to map DNA datasets to a given reference genome using BWA MEM and Samtools.	snakemake snakemake-workflows genomics bioinformatics ngs-pipeline workflows	last update 2024-11-21formatting: failedlinting: failed	1	4
3d-omics/hg_genotype	No description available.		last update 2024-11-30formatting: passedlinting: failed	1	1
tdayris/fair_gatk_mutect2	Snakemake workflow used to call germline and/or somatic variants with GATK Mutect2	fair gatk-bestpractices mutect2 reproducible-workflows snakemake snakemake-workflow variant-calling	last update 2024-07-22formatting: failedlinting: passed	1	2
mariaelf97/amplicon_sequencing_simulator	Amplicon read simulation pipeline		last update 2024-08-02formatting: passedlinting: passed	1	0
frattalab/QAPA_snakemake	Snakemake pipeline to run QAPA and perform differential polyA site usage analysis		last update 2024-07-31formatting: failedlinting: failed	1	3
spjuhel/BoARIO-Sensitivity	Sensitivity Analysis of BoARIO		last update 2024-08-08formatting: failedlinting: failed	1	1
metagenome-atlas/metagenome-assembly	Workflow module for metagenome assembly		last update 2024-06-25formatting: failedlinting: failed	1	1
fcaretti/SNPs_from_RNA	A Snakemake workflow to call variants (SNPs) from bulk RNA-seq samples		last update 2024-06-22formatting: passedlinting: passed	1	1
richardstoeckl/basecallNanopore	Snakemake Pipeline to automatically basecall Nanopore sequencing data with hybrid approach of simple…		last update 2024-05-27formatting: failedlinting: failed	1	1
monagrland/MB_Pipeline	Metabarcoding Pipeline for Illumina Sequencing Data		last update 2024-05-21formatting: passedlinting: failed	1	3
wharvey31/denovo_sv_validation	Pipeline for validation of de novo SVs		last update 2024-04-23formatting: failedlinting: failed	1	1
juliawiggeshoff/AugusMake	The AugusMake pipeline is a Snakemake-based workflow for generating gene annotations using the Augus…	augustus gene-prediction reproducibility rna-seq snakemake transcriptome-assembly workflow	last update 2024-03-07formatting: failedlinting: failed	1	1
hreypar/felicidades	Repositorio para darle un pastel de cumpleaños a tus amix		last update 2023-10-03formatting: failedlinting: passed	1	1
vembrane/vembrane-benchmark	benchmark workflow for vembrane paper		last update 2023-01-23formatting: passedlinting: passed	1	2
lacklab/MuSTARRd	(Analysis of Saturation) Mu(tagenesis) STARR(seq) d(ata)	bioinformatics sequencing starrseq ngs snakemake	last update 2023-02-15formatting: passedlinting: failed	1	1
Jain-Joyce-Labs/snakemake-chipseq	Pipeline for processing ChIP-seq experiments. CURRENTLY IN ALPHA. Not ready for prime time.		last update 2022-12-15formatting: failedlinting: failed	1	0
jjjoelle/learn_rna	No description available.		last update 2023-01-10formatting: failedlinting: failed	1	1
TLenfers/multispecies_mitochondrial_variant_analysis	This workflow performs a variant analysis on mitochondrial genomes using the bcftools variant caller…	snakemake reproducibility mitochondrial-variants	last update 2022-07-14formatting: passedlinting: passed	1	1
mrvollger/sd-divergence	No description available.		last update 2022-03-24formatting: passedlinting: failed	1	1
IMS-Bio2Core-Facility/polya_liftover	A Snakemake Workflow for using PolyA_DB and UCSC LiftOver with CellRanger	bioinformatics-pipeline snakemake cellranger liftover workflow single-cell-rna-seq reproducibility python shell transcriptomics fastqc multiqc	last update 2022-02-20formatting: passedlinting: passed	1	1
IMS-Bio2Core-Facility/GTExSnake	A fully concurrent pipeline for querying transcript-level GTEx data in specific tissues	bioinformatics snakemake reproducible-science conda singularity multithreading pipeline	last update 2021-10-28formatting: failedlinting: passed	1	1
IMS-Bio2Core-Facility/single_snake_sequencing	A Snakemake workflow for standardised sc/snRNAseq analysis	bioinformatics snakemake scrna-seq reproducible-science conda singularity	last update 2021-11-02formatting: passedlinting: passed	1	1
koesterlab/ngs-fastq-to-cram	Snakemake workflow for converting FASTQ files to self-contained CRAM files with maximum lossless com…		last update 2021-12-16formatting: failedlinting: passed	1	0
jma1991/chromium	A Snakemake workflow to process scRNA-seq data from 10x Genomics	snakemake	last update 2021-08-12formatting: failedlinting: failed	1	1
nikostr/dna-seq-deepvariant-glnexus-variant-calling	A Snakemake workflow for variant calling with DeepVariant, and optionally joint variant calling usin…	genomic-variant-calling deepvariant sciworkflows snakemake reproducibility	last update 2021-06-30formatting: passedlinting: passed	1	2
Ovewh/ACP-haugvaldstad-et-al-2025	Source code for the analysis related to Haugvaldstad et al 2025, ACP		last update 2025-03-04formatting: failedlinting: failed	0	1
kr-colab/popgensbi_snakemake	Snakemake workflow for popgensbi		last update 2025-03-03formatting: failedlinting: failed	0	4
orthanq/orthanq-hla-quantification	A Snakemake workflow for typing and quantifying HLAs using Orthanq.		last update 2025-03-07formatting: failedlinting: failed	0	0
nate-d-olson/giab-stvar-curation-table	No description available.		last update 2025-03-06formatting: failedlinting: failed	0	1
abbyevewilliams/map-pipeline	A snakemake pipeline for mapping next generation sequencing reads from avian museum samples.		last update 2025-03-05formatting: failedlinting: failed	0	1
kevinrue/snakemake-cncb-ensembl-2024	No description available.		last update 2025-03-07formatting: failedlinting: failed	0	1
tdayris/fair_macs2_calling	Snakemake workflow used to call peaks with Macs2	bowtie2 homer macs2 sambamba snakemake snakemake-workflow snakemake-wrappers	last update 2025-03-07formatting: passedlinting: passed	0	1
tdayris/fair_genome_indexer	Download and index Ensembl sequences and annotations, remove non-canonical chromosimes, remove low T…	ensembl fair snakemake snakemake-workflow snakemake-wrappers	last update 2025-03-07formatting: passedlinting: passed	0	1
cmc-aau/snakemake_project_template	Testing snakemake		last update 2025-02-25formatting: failedlinting: failed	0	1
baerlachlan/smk-rnaseq-counts	Snakemake workflow for estimating read counts from RNA-seq data		last update 2025-02-27formatting: passedlinting: failed	0	1
abbyevewilliams/vc-pipeline	A pipeline for variant calling using ANGSD.		last update 2025-02-26formatting: failedlinting: passed	0	1
loganylchen/prep-bonito-training-data	No description available.		last update 2025-02-26formatting: failedlinting: failed	0	1
loganylchen/prep_public_nanoporeDRS_data	No description available.		last update 2025-02-26formatting: failedlinting: failed	0	1
BesenbacherLab/bbq_pipeline	Snakemake workflow for the Better Base Quality (BBQ) tool		last update 2025-02-28formatting: failedlinting: failed	0	2
shahcompbio/proteomegenerator-smk	Snakemake workflow for proteomegenerator Isabl app		last update 2025-02-17formatting: failedlinting: failed	0	0
shahcompbio/transdecoder-smk	snakemake pipeline for transdecoder		last update 2025-02-17formatting: failedlinting: failed	0	0
flo-schu/pymob-workflow	Snakemake workflow for running end-to-end parameter inference, including customizable reporting		last update 2025-02-19formatting: failedlinting: failed	0	1
petroskilp/clustromics	No description available.		last update 2025-02-18formatting: failedlinting: failed	0	1
aekrylova/scPASU	No description available.		last update 2025-02-21formatting: failedlinting: failed	0	1
hzi-bifo/phylogeny-of-single-cells	snakemake workflow for the phylogenetic reconstruction of single cell lineages from multiple displac…		last update 2025-02-11formatting: failedlinting: failed	0	6
Bioinflows-Bioversity-CIAT/tm-shift_designer	A workflow intended to perform the design of tm-shift primers for genotype SNPs		last update 2025-02-13formatting: failedlinting: passed	0	0
dlaehnemann/create-ecdna-testing-data	A Snakemake workflow for creating testing data for ecDNA analysis workflows: long reads (Nanopore wi…	circular-dna ecdna illumina-sequencing nanopore-reads snakemake workflow simulation	last update 2025-02-12formatting: passedlinting: passed	0	1
shahcompbio/bambu-smk	Snakemake workflow for transcript assembly with Bambu		last update 2025-02-14formatting: failedlinting: failed	0	0
tdayris/fair_rnaseq_salmon_quant	Snakemake workflow designed to perform RNASeq transcrpotime expression estimation with Salmon	fair rnaseq-pipeline snakemake snakemake-workflow reproducible-science	last update 2025-02-05formatting: passedlinting: passed	0	1
AntonJMLarsson/lustre_snakemake_pipeline	A snakemake workflow for analyzing LUSTRE data.		last update 2025-01-30formatting: failedlinting: failed	0	1
SveTho/merge_fastqs	merge fastq based on unit sheet		last update 2025-01-22formatting: failedlinting: failed	0	1
joyling93/sc10x_wf	No description available.		last update 2025-01-16formatting: failedlinting: failed	0	1
ethan-baldwin/hybpiper_astral_pipeline	A snakemake pipeline to use hybpiper and ASTRAL to get a species tree from a set of reads.		last update 2025-01-19formatting: failedlinting: failed	0	0
mdondrup/ras_meta_transcriptomics	No description available.		last update 2025-01-17formatting: failedlinting: failed	0	1
ethan-baldwin/braker3_annotation	A snakemake workflow for annotating genome assemblies with braker3		last update 2024-12-17formatting: failedlinting: failed	0	1
spjuhel/Climada_TC_TCSurge_Generation	Generating consistent TC and TC Surge hazard set event using Snakemake and CLIMADA		last update 2024-12-17formatting: failedlinting: failed	0	1
guyer/slurm_conda_glitch	Minimal Reproducible Example of snakemake slurm executor plugin not handling conda environments		last update 2024-12-17formatting: failedlinting: failed	0	1
watronfire/Gloucester	Workspace for phenotype-genotype comparison of Vibrio cholerae		last update 2024-10-29formatting: failedlinting: passed	0	1
Gmidtg21/bt7-9gmidtg	No description available.		last update 2024-11-08formatting: failedlinting: failed	0	1
Oliver-Christian-Larsen/BT7-9GenomeAssembly	12		last update 2024-11-08formatting: failedlinting: failed	0	1
MaNyh/NTRFlows	No description available.		last update 2024-11-04formatting: failedlinting: failed	0	2
vince-fang/basic	No description available.		last update 2024-10-31formatting: failedlinting: passed	0	1
vince-fang/test	No description available.		last update 2024-10-31formatting: failedlinting: passed	0	1
fmi-basel/ggiorget_ms2analysis	No description available.		last update 2024-11-14formatting: failedlinting: failed	0	6
Louis-XIV-bis/NJ_tree_bootstrap	No description available.		last update 2024-11-12formatting: failedlinting: passed	0	1
mdondrup/admixture_workflow	No description available.		last update 2024-11-12formatting: failedlinting: failed	0	1
solida-core/astra	Snakemake pipeline to performs Variant Calling (with DeepVariant) and Variant Annotation (with VEP…		last update 2024-11-21formatting: failedlinting: failed	0	3
kevinrue/snakemake-cncb-2024	No description available.		last update 2024-11-20formatting: failedlinting: failed	0	2
markschl/uvsnake	USEARCH/VSEARCH-based pipeline for amplicon data processing		last update 2024-11-20formatting: passedlinting: passed	0	2
lacklab/epens-snakemake	Snakemake pipeline for the analysis of ePENS (ChIP-exo) data		last update 2024-11-18formatting: failedlinting: failed	0	2
nate-d-olson/giab-sv-external-eval	No description available.		last update 2024-11-18formatting: failedlinting: passed	0	1
kr1stoff/KML-RNASEQ	No description available.		last update 2024-11-27formatting: passedlinting: failed	0	1
karltayeb/laplace-bfs	A systematic comparison of Bayes factor approximations		last update 2024-11-21formatting: failedlinting: failed	0	1
kevinrue/snakemake-cncb-3	Third version of the pipeline		last update 2024-12-02formatting: failedlinting: failed	0	1
MathiasEskildsen/ONT_RNA-seq_wf	Workflow for processing ONT RNA-seq data (direct cDNA and PCR cDNA sequencing kits) for differential…		last update 2024-12-02formatting: failedlinting: failed	0	1
jsquaredosquared/novocraft-sv-benchmarking	Comparing performance of SV callers when using NovoAlign vs other aligners.	sv-calling novoalign	last update 2024-11-29formatting: failedlinting: failed	0	1
tdayris/fair_cnv_facets	Snakemake workflow designed to call CNV using Facets		last update 2024-12-09formatting: failedlinting: failed	0	1
nezapajek/project-tobamo	Preparation of a curated catalogue of sequences of possible new tobamoviruses by scanning a large ac…		last update 2024-12-09formatting: passedlinting: failed	0	1
young5454/ABComp	ABComp : Assembly Polishing and Bacterial Whole-genome Comparison Pipeline for Multi-group Clinical …		last update 2024-12-07formatting: failedlinting: failed	0	1
mrvollger/DSA-phasing	No description available.		last update 2024-12-04formatting: passedlinting: failed	0	1
Xavster838/downstream_isoseq_process	process aligned isoseq libraries to: 1. identify consensus gene models ; 2. compare gene model maint…		last update 2024-12-12formatting: failedlinting: failed	0	1
tdayris/fair_bowtie2_mapping	Align reads over a reference genome, filter aligned-reads, and mark duplicates	bowtie2 multiqc sambamba snakemake snakemake-workflow snakemake-wrappers	last update 2024-12-13formatting: passedlinting: failed	0	1
tdayris/fair_fastqc_multiqc	Perform basic QC over sequenced data	fair fastqc fastqscreen reproducible-workflows snakemake	last update 2024-12-13formatting: passedlinting: failed	0	1
alzel/refseq_pipeline	No description available.		last update 2024-08-23formatting: failedlinting: failed	0	1
mdondrup/admixture_simulation	No description available.		last update 2024-08-23formatting: failedlinting: failed	0	1
mdondrup/test	No description available.		last update 2024-08-22formatting: failedlinting: passed	0	1
baerlachlan/smk-rnaseq-gatk-variants	Snakemake implementation of the GATK best-practices workflow for RNA-seq short variant discovery		last update 2024-08-22formatting: failedlinting: failed	0	1
percyfal/tswf-smk	Tree sequence workflow		last update 2024-08-21formatting: failedlinting: passed	0	1
LET19/snakemake-template	No description available.		last update 2024-08-20formatting: failedlinting: passed	0	1
bethanyyk/DENV_simulations	No description available.		last update 2024-09-05formatting: passedlinting: passed	0	1
cmc-aau/nanopore_16Samp	Snakemake workflow to process 16S nanopore amplicon sequences (of any length) and produce an abundan…		last update 2024-08-26formatting: failedlinting: failed	0	3
niekwit/rna-seq-star-deseq2	Snakemake workflow for RNA-Seq differential transcript analysis using STAR/Deseq2		last update 2024-09-06formatting: failedlinting: failed	0	1
gonzarizzo/globe_map	The aim of this repository is to practice on how to create a workflow that allows automatic creation…		last update 2024-09-05formatting: failedlinting: passed	0	1
mdondrup/divergence_time	No description available.		last update 2024-09-04formatting: failedlinting: failed	0	1
loganylchen/snakemake-epitranscriptome	No description available.		last update 2024-09-13formatting: failedlinting: passed	0	1
vkpat/short-read-mapping-and-QC-snakemake-pipeline	No description available.		last update 2024-09-11formatting: failedlinting: failed	0	1
niekwit/chip-seq	Snakemake workflow for ChIP-Seq analysis		last update 2024-09-20formatting: failedlinting: failed	0	1
simonmoulds/subseasonal-flood-prediction	No description available.		last update 2024-08-02formatting: failedlinting: failed	0	1
charleshefer/snakemake-workflow-template	Template from Snakemake		last update 2024-07-30formatting: failedlinting: passed	0	1
SveTho/bcl2fastq2_workflow	No description available.		last update 2024-08-14formatting: failedlinting: passed	0	1
spjuhel/BoARIO-MRIOT-Tools	Pipelines to parse and aggregate MRIOT data for BoARIO		last update 2024-08-09formatting: failedlinting: failed	0	1
simonmoulds/india-crop-atlas	No description available.		last update 2024-08-16formatting: failedlinting: passed	0	1
koesterlab/rossi-ips-dmr	Calling and plotting of differentially methylated regions between two or more biological samples in …		last update 2024-08-15formatting: passedlinting: failed	0	0
Addimator/compare_meth	No description available.		last update 2024-08-15formatting: passedlinting: failed	0	1
mukherjeelab/CLIPs4U	Snakemake workflow for PAR-CLIP data analysis		last update 2024-07-12formatting: failedlinting: failed	0	2
weizhu365/snakemake_template_test	Test		last update 2024-07-11formatting: failedlinting: passed	0	1
W-L/megahit_metagenome_assembly_binning	JMF workflow		last update 2024-07-10formatting: failedlinting: passed	0	1
solida-core/musta	MUSTA: a modular pipeline to detect, classify and interpret mutations in cancer		last update 2024-07-05formatting: failedlinting: passed	0	4
ArsenaultResearch/windowRAxMLng	Generate a series of windowed phylogenies with associated metrics based on a .vcf input		last update 2024-07-05formatting: failedlinting: failed	0	1
SilasK/Snakebread	No description available.		last update 2024-07-05formatting: failedlinting: failed	0	1
SilasK/Metagenome-QC	Snakmake-workflow for qc		last update 2024-07-05formatting: failedlinting: failed	0	1
CAST-genomics/snakemake-gfa-complexity	No description available.		last update 2024-07-02formatting: failedlinting: failed	0	1
elsamah/ExomeSeq	No description available.		last update 2024-06-21formatting: failedlinting: failed	0	1
votti/snakemake-renv-quarto	An example repository for combining snakemake, renv and quarto		last update 2024-06-19formatting: passedlinting: passed	0	1
davelunt/badseqs	testing programs with fasta poison files		last update 2024-06-19formatting: failedlinting: passed	0	1
mushu-bytes/scelect	Snakemake Pipeline for S(c)electing Normalization and Integration Methods for Single Cell Analysis		last update 2024-06-14formatting: failedlinting: failed	0	1
manuelphilip/Single-cell-analysis-Snakemake-workflow	A Snakemake workflow for analysing single cell data obtained from Cell ranger platform using Seurat …	cellranger seurat single-cell celltype-identification differential-expression	last update 2024-06-14formatting: failedlinting: passed	0	1
loganylchen/prep_mix_data	No description available.		last update 2024-06-11formatting: failedlinting: failed	0	1
tavareshugo/smk-indexer	Snakemake workflow for indexing reference genomes		last update 2024-06-07formatting: failedlinting: failed	0	1
mynameisdidit/UTS_Bioinformatika_SV-Callers	No description available.		last update 2024-05-31formatting: failedlinting: failed	0	1
merfre/Hull_Microbiome_Cluster_Workflow	Snakemake workflow for microbiome research cluster analysis using fastp, Kraken2, and BIOM.		last update 2024-05-27formatting: failedlinting: failed	0	1
arwisyah/snakemake_rna_vc_docker_reproduce	No description available.		last update 2024-05-25formatting: passedlinting: passed	0	1
RaphaelAngerbauer/snakemake_template	No description available.		last update 2024-05-24formatting: failedlinting: passed	0	1
loganylchen/NanoRNAMod	No description available.		last update 2024-05-24formatting: failedlinting: failed	0	1
nikostr/read-mapping	Snakemake module for read mapping using BWA-MEME, pbmm2 or minimap2. Experimental.		last update 2024-05-23formatting: failedlinting: failed	0	1
lparsons/pf15-smallrna-rseto	Pf15 Small RNA-Seq analysis for Murphy Lab - Renee Seto Apr 2, 2024		last update 2024-05-22formatting: passedlinting: failed	0	1
regevs/tadpoles	Workflow to detect recombinant reads from long read sequencing data		last update 2024-05-15formatting: failedlinting: passed	0	1
Phlya/tagmap	Map insertions of transopable elements using tagmentation		last update 2024-05-08formatting: failedlinting: failed	0	1
cmkobel/smktest	No description available.		last update 2024-04-25formatting: failedlinting: passed	0	1
snakemake-workflows/dna-seq-short-read-circle-map	A snakemake workflow for calling extrachromosomal circular DNA in Illumina short-read sequencing dat…		last update 2024-04-23formatting: passedlinting: passed	0	2
WHops/triopull-asm	A snakemake workflow for pulling reads out of a trio of bamfiles, and making a local assembly using …		last update 2024-04-12formatting: failedlinting: failed	0	1
jjjermiah/snakemake_template	No description available.		last update 2024-04-08formatting: failedlinting: passed	0	1
Wytamma/snk-basic-pipeline	An example pipeline that can be installed with snk		last update 2022-12-23formatting: failedlinting: passed	0	1
kreczko/cms-public-tutorial-snakemake	No description available.		last update 2024-04-04formatting: failedlinting: passed	0	1
vivekbibs/pipeline_template	No description available.		last update 2024-04-03formatting: failedlinting: passed	0	1
NicholasHattrup/MDPilot	No description available.		last update 2024-04-01formatting: failedlinting: failed	0	1
ArsenaultResearch/RNAseq_Pipeline	Test pipeline for performing RNA-seq analysis with STAR from raw reads to counts files.		last update 2022-12-29formatting: failedlinting: passed	0	1
ArzooShamoon/CellRanger	No description available.		last update 2024-03-07formatting: failedlinting: passed	0	1
dlaehnemann/demo-standardized-workflow	No description available.		last update 2024-03-07formatting: failedlinting: passed	0	1
BioCoderR/scaling-clam	No description available.		last update 2024-03-07formatting: failedlinting: passed	0	1
SilasK/Metagenome-Profile	No description available.		last update 2024-01-22formatting: failedlinting: failed	0	1
NeuroGranberg/NODDIpipeline	No description available.		last update 2024-02-28formatting: failedlinting: failed	0	1
dlaehnemann/rna-seq-conservative-fold-change-without-replicates	snakemake workflow to determine conservative fold changes between transcriptomic samples when no bio…		last update 2024-02-14formatting: passedlinting: passed	0	1
IKIM-Essen/QC_pre_NextSeq	Workflow for short quality control of MiSeq sequencing data before sequencing on high throughput dev…		last update 2024-02-07formatting: passedlinting: passed	0	1
dlaehnemann/evaluate_varlociraptor_purity_estimation	A little snakemake workflow to evaluate the varlociraptor subcommand estimate contamination.		last update 2024-02-06formatting: failedlinting: passed	0	1
usnistgov/giab-defrabb	Genome In A Bottle Development Framework for Assembly Based Benchmarks		last update 2024-02-02formatting: failedlinting: passed	0	3
isaacvock/PROseq_etal	PRO-seq + ChIP-seq pipeline, with potential NET-seq/ATAC-seq/etc. extensions		last update 2024-01-26formatting: passedlinting: passed	0	1
belowlab/ukbb-phecode-mapping	Snakemake pipeline for reproducibly mapping the ICD codes in UK Biobank datasets to Phecodes		last update 2024-02-01formatting: failedlinting: passed	0	2
Matheusdras/Snakemake-template	No description available.		last update 2024-03-25formatting: failedlinting: passed	0	1
dlaehnemann/create-quant-seq-testing-dataset	A Snakemake workflow for (reproducibly) creating a QuantSeq 3’ mRNA testing dataset that is both sma…		last update 2024-01-26formatting: failedlinting: failed	0	1
xiayh17/benchmark_scomatic	a benchmakr. start from the scomatic		last update 2024-01-24formatting: failedlinting: passed	0	1
dlaehnemann/create-sv-ci-testing-dataset	a mini snakemake workflow to produce structural variant testing dataset small enough for CI systems,…		last update 2023-10-27formatting: failedlinting: passed	0	1
UpalabdhaD/snakemake_wf_skeleton	No description available.		last update 2024-01-17formatting: failedlinting: passed	0	1
bakerwm/snakemake-rnaseq-star	Snakemake workflow for RNAseq using STAR and DESeq2		last update 2023-12-26formatting: failedlinting: failed	0	1
ezherman/example-workflow	No description available.		last update 2023-12-21formatting: passedlinting: passed	0	1
Princeton-LSI-ResearchComputing/hifi-assembly	Assemble HiFi reads from PacBio		last update 2023-12-19formatting: failedlinting: passed	0	1
zhongmicai/mosaicatcher-pipeline	Structural variant calling from single-cell Strand-seq data		last update 2023-12-14formatting: failedlinting: passed	0	1
mbquashie/tm	No description available.		last update 2023-12-13formatting: failedlinting: passed	0	1
varlociraptor/varlociraptor-methylation-evaluation	No description available.		last update 2023-08-15formatting: failedlinting: passed	0	1
nate-d-olson/defrabb	Development Environment For Assembly Based Benchmarks		last update 2023-01-10formatting: failedlinting: failed	0	1
Ovewh/Climaso	The CLimate IMpact of AeroSOls: forcing and feedbacks		last update 2023-05-03formatting: failedlinting: failed	0	1
dawidkrzeciesa/dna-seq-cnv	No description available.		last update 2023-08-30formatting: failedlinting: failed	0	2
rcavalcante/test_snakemake_pipeline	No description available.		last update 2023-11-02formatting: failedlinting: passed	0	1
loganylchen/snakeRIP	No description available.		last update 2023-11-16formatting: failedlinting: passed	0	1
alexhbnr/contig_simulation	No description available.		last update 2023-11-10formatting: failedlinting: passed	0	1
garrison-chen/SR-pipe	No description available.		last update 2023-11-22formatting: failedlinting: passed	0	1
seankmartin/atn-sub-lfp-workflow	Working with snakemake for analysis of SUB LFP		last update 2023-03-10formatting: failedlinting: passed	0	2
jackieduckie/methylation-capture	No description available.		last update 2023-12-06formatting: failedlinting: passed	0	1
nate-d-olson/adotto-smk	A snakemake based pipeline to build Adotto TR databases		last update 2023-10-09formatting: passedlinting: passed	0	1
poloarol/snakemake-methylseq	A snakemake pipeline to process methylation data obtain through bisulfite and enzymatic methyl seque…		last update 2023-10-16formatting: failedlinting: failed	0	1
hreypar/containers_test	Test running rules in a container		last update 2023-10-13formatting: failedlinting: failed	0	1
ubercomrade/cut_and_run_analysis	No description available.		last update 2023-10-11formatting: failedlinting: passed	0	1
kpalin/ONT_hg_somatic	Somatic variant calling for ONT WGS cancer data		last update 2023-09-25formatting: failedlinting: passed	0	1
jianhong/pairedtag	A snakemake workflow for single-cell multiomic data analysis pipeline		last update 2023-07-19formatting: failedlinting: failed	0	1
Phlya/distill-reorder-C	snakemake workflow to analyze Hi-C-like data for multiple versions of the reference genome		last update 2023-06-07formatting: failedlinting: passed	0	2
emmaewade/pangenome-workflow	A Snakemake workflow for microbial pangenomics analyses.	abyss bioperl pangenomics roary snakemake microbial-genomics	last update 2023-06-25formatting: failedlinting: failed	0	1
Wheeler-Lab/InDelCoordinateCorrection	No description available.		last update 2023-06-23formatting: failedlinting: failed	0	2
khersameesh24/snakemake-workflow-template	A template repo for a snakemake project		last update 2023-06-23formatting: failedlinting: passed	0	2
simonmoulds/us-streamflow-prediction	Experiments on deep learning for streamflow prediction in the US		last update 2022-09-13formatting: failedlinting: passed	0	1
drifter089/pypsa-workflow	No description available.		last update 2023-06-09formatting: failedlinting: passed	0	1
johnne/map_metaT	Snakemake workflow to map and quantify metatranscriptomic data using a metagenome reference		last update 2022-03-28formatting: failedlinting: failed	0	0
giacatxt/trimmomatic	No description available.		last update 2023-05-17formatting: failedlinting: passed	0	2
giacatxt/gatk	No description available.		last update 2023-05-10formatting: failedlinting: passed	0	1
simonmoulds/gwm-analysis	No description available.		last update 2022-11-02formatting: failedlinting: passed	0	1
gabora/snakemake_template	template folder structure		last update 2023-05-05formatting: failedlinting: passed	0	1
crs4/fair-crcc-get-data	No description available.		last update 2022-10-27formatting: failedlinting: failed	0	13
tbenavi1/RetroDetector	A pipeline for identifying fixed and segregating retrocopies from short- and long-read whole genome …		last update 2022-06-09formatting: failedlinting: failed	0	2
robingarcia/test_snake	Einfach nur zum test.		last update 2023-04-18formatting: failedlinting: passed	0	1
recervictory/rna-seq-test	RNA seq Pipeline		last update 2023-04-03formatting: failedlinting: passed	0	1
loganylchen/RNA-seq-analysis-pipeline	No description available.		last update 2023-03-28formatting: failedlinting: passed	0	1
nixonlab/HERV_um_mets	HERV analysis in UM metastasis		last update 2023-03-20formatting: failedlinting: failed	0	1
Phlya/C-integration-mapping	[wip] mapping integration sites of defined sequences using Hi-C-like data		last update 2023-03-17formatting: failedlinting: passed	0	1
IKIM-Essen/ResMAG	Snakemake workflow for metagenomic assembly, binning and finding of antibiotic resistance		last update 2023-03-17formatting: failedlinting: passed	0	1
massiddamt/rna_vc_docker	A Snakemake pipeline for RNA Seq Variant Calling	pipeline rnaseq snakemake-workflow	last update 2023-03-05formatting: passedlinting: passed	0	1
kaminosekai54/snakemakeTest	No description available.		last update 2023-03-13formatting: failedlinting: passed	0	1
dbespiatykh/TBvar	Variant detection and lineage barcoding of Mycobacterium tuberculosis	barcoding mycobacterium-tuberculosis snakemake variant-calling	last update 2023-01-26formatting: passedlinting: passed	0	1
trickovicmatija/kingfisher_workflow	This is a workflow that allows you to download whole projects and metadata with kingfisher. Addition…		last update 2022-11-09formatting: failedlinting: failed	0	1
simonmoulds/uk-decadal-flood-prediction	No description available.		last update 2023-01-31formatting: failedlinting: failed	0	1
DSiB-G2/G2-CovPipeline	An easy to use pipeline for assigning lineages to SARS-CoV-2 (COVID) Next-Generation Sequencing data…		last update 2023-02-09formatting: failedlinting: passed	0	0
mrvollger/k-mer-variant-phasing	No description available.		last update 2023-05-04formatting: failedlinting: failed	0	1
cjgunnar/snake-dreem	SnakeMake workflow for DREEM, the clustered MaPseq analysis		last update 2023-02-03formatting: failedlinting: passed	0	1
nixonlab/snakemake_rule_library	A place to share generic best practices rules for the lab		last update 2023-01-09formatting: failedlinting: passed	0	1
WanlinLi2021/demo	No description available.		last update 2023-01-27formatting: failedlinting: passed	0	1
matinnuhamunada/interproscan_helper	A snakemake pipeline to run interproscan locally		last update 2023-01-20formatting: failedlinting: failed	0	1
valentynbez/FuncMi	No description available.		last update 2023-01-19formatting: failedlinting: passed	0	1
simonmoulds/jules-mosart	No description available.		last update 2022-11-07formatting: failedlinting: failed	0	1
zifornd/arrays	A Snakemake workflow to analyse Affymetrix expression arrays	snakemake microarray	last update 2022-12-30formatting: failedlinting: failed	0	0
Sara-Morsy/metaomic-workflow	No description available.		last update 2022-12-25formatting: failedlinting: passed	0	1
simonmoulds/decadal-prediction-data-preparation	No description available.		last update 2022-08-23formatting: failedlinting: passed	0	1
SichongP/atac-seq	Snakemake workflow for ATAC-seq analysis		last update 2022-05-05formatting: failedlinting: failed	0	1
rmFlynn/snakemake_example	No description available.		last update 2022-07-12formatting: failedlinting: failed	0	1
AmberFu/snakemake_BAMmetrics_mosdepth	Sample QC - For generating BAM metrics using mosdepth		last update 2022-11-08formatting: failedlinting: failed	0	1
simonmoulds/jules-ganges-data-preparation	No description available.		last update 2022-11-02formatting: failedlinting: passed	0	1
omidalam/can_vac	A Snakemake pipeline for SNV detection in cancer samples		last update 2022-08-20formatting: failedlinting: passed	0	1
rmFlynn/dram_validataion_pipline	No description available.		last update 2022-10-18formatting: failedlinting: passed	0	1
panguangze/trio_call_phase_pipeline	No description available.		last update 2022-09-07formatting: failedlinting: failed	0	1
kvntrc/snakemake_template	No description available.		last update 2022-09-21formatting: failedlinting: passed	0	1
yeyuan98/rna_fish_analysis	RNA-FISH analysis snakemake workflow		last update 2022-09-12formatting: failedlinting: failed	0	1
seung1yoo/snakemake-s3-prototype	No description available.		last update 2022-09-06formatting: failedlinting: passed	0	1
simonmoulds/uk-decadal-flood-prediction-lstm	No description available.		last update 2022-09-01formatting: failedlinting: failed	0	1
knutdrand/bionumpy-benchmarks	Snakemake workflow for running benchmarks for bionumpy		last update 2022-08-22formatting: failedlinting: passed	0	2
Cesconlab/ExomeSeq	No description available.		last update 2022-08-23formatting: failedlinting: failed	0	0
trickovicmatija/assign-MAGs	No description available.		last update 2022-08-15formatting: failedlinting: failed	0	1
elsamah/ExomeSeq_wNorm	No description available.		last update 2022-01-06formatting: failedlinting: failed	0	1
Xavster838/get_and_annotate_locus	No description available.		last update 2022-07-19formatting: passedlinting: passed	0	1
KonstantinBurkin/cbai	No description available.		last update 2022-07-13formatting: failedlinting: failed	0	1
Albinam1/bioinformatics_school	No description available.		last update 2022-07-13formatting: failedlinting: failed	0	1
Xavster838/coreDupGraph	No description available.		last update 2022-06-23formatting: failedlinting: failed	0	1
osvaldoreisss/rnaseq_analysis_kallisto_deseq2	No description available.		last update 2022-06-27formatting: failedlinting: passed	0	1
t-i-r/snakemake-workflow-template	Template to create skeleton for snakemake		last update 2022-06-12formatting: failedlinting: passed	0	1
Xavster838/run_NucFreq	No description available.		last update 2022-05-09formatting: passedlinting: passed	0	1
rmFlynn/DRAM_testing_pipline	No one has time to test all the ways dram is used least of all me, so this pipeline will do it for m…		last update 2022-05-06formatting: failedlinting: passed	0	1
radlinsky/snakemake_scrape_house_data	No description available.		last update 2022-05-01formatting: failedlinting: passed	0	1
davidlorenz/snakemake-workflow-template	https://github.com/snakemake-workflows/snakemake-workflow-template		last update 2022-04-20formatting: failedlinting: passed	0	1
SilkeAllmannLab/pacbio_snakemake	A Snakemake pipeline to go from raw .subreads.bam PacBio ISO-Seq to assembled mRNA isoforms (FASTA f…		last update 2022-06-28formatting: failedlinting: passed	0	2
gbucci/CNVkit	No description available.		last update 2022-02-17formatting: failedlinting: failed	0	1
CBIbigA/hicstuff_pipeline	hicstuff_pipeline		last update 2022-02-17formatting: failedlinting: failed	0	2
clarajegousse/hanoxy	No description available.		last update 2022-05-26formatting: failedlinting: failed	0	1
hzi-bifo/snakemake-workflow-univec-removal	A small Snakemake workflow to remove contaminating vector sequences from raw sequencing data using U…		last update 2022-02-03formatting: failedlinting: passed	0	6
WestGermanGenomeCenter/circrna_detection	circs_snake : a snakemake-based circRNA detection workflow	circular rna rna-seq rna-seq-pipeline rnaseq-pipeline	last update 2021-09-30formatting: failedlinting: failed	0	1
plycrsk/rna-seq-star-deseq2	No description available.		last update 2022-01-18formatting: passedlinting: passed	0	1
thomasbtf/sars-cov-2-wbe	Quantifying SARS-CoV-2 lineage abundances in wastewater.	sars-cov-2 lineage abundance wastewater	last update 2021-12-01formatting: passedlinting: passed	0	1
rochevin/RNA-seq-from-SRR-single	No description available.		last update 2022-02-15formatting: failedlinting: failed	0	1
Xavster838/assembly_validation	No description available.		last update 2021-09-09formatting: passedlinting: passed	0	1
jma1991/rnaseq	A workflow for RNA-seq analyses in Snakemake	rnaseq snakemake	last update 2021-07-11formatting: failedlinting: failed	0	1