Ecosyste.ms: Repos

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

Package Usage: actions: nf-core/setup-nextflow

Install Nextflow and add it to the PATH
13 versions
Latest release: 7 months ago

View more package details: https://packages.ecosyste.ms/registries/github%20actions/packages/nf-core/setup-nextflow

View more repository details: https://repos.ecosyste.ms/hosts/GitHub/repositories/nf-core%2Fsetup-nextflow

Dependent Repos 300

seqan/raptor
A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.
  • v1 .github/workflows/ci_workflows.yml

Size: 3.9 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

nf-core/metapep
From metagenomes to epitopes and beyond
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 8.12 MB - Last synced: about 9 hours ago - Pushed: 1 day ago

ewels/nf-core-tools Fork of nf-core/tools
See the main fork of this repository here >>>
  • v1 .github/workflows/create-lint-wf.yml
  • v1 .github/workflows/create-test-wf.yml
  • v1 .github/workflows/pytest-frozen-ubuntu-20.04.yml
  • v1 .github/workflows/pytest.yml
  • v1 .github/workflows/rich-codex.yml
  • v1 .github/workflows/sync.yml

Size: 15.6 MB - Last synced: about 8 hours ago - Pushed: 1 day ago

sanger-tol/genomeassembly
Implementation of ToL genome assembly workflows
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 46.1 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

nf-core/circrna
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 61.8 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

beiko-lab/arete
AMR/VF LGT focused bacterial genomics analysis workflow
  • v1 .github/workflows/test.yml

Size: 36.7 MB - Last synced: about 5 hours ago - Pushed: about 6 hours ago

fulcrumgenomics/nf-core-demultiplex Fork of nf-core/demultiplex
Demultiplexing pipeline for sequencing data
  • v1 .github/workflows/linting.yml

Size: 12.3 MB - Last synced: 10 days ago - Pushed: about 1 year ago

nf-core/mhcquant
Identify and quantify MHC eluted peptides from mass spectrometry raw data
  • v1 .github/workflows/linting.yml
  • v1 .github/workflows/ci.yml

Size: 24 MB - Last synced: 1 day ago - Pushed: 1 day ago

nf-core/proteinfold
Protein 3D structure prediction pipeline
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 5.58 MB - Last synced: 2 days ago - Pushed: 2 days ago

nf-cmgg/preprocessing
Preprocessing workflow for sequencing data at CMGG
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 6.63 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

sanger-tol/ensemblrepeatdownload
Nextflow pipeline to download repeat annotations from Ensembl onto the Tree of Life directory structure
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 2.44 MB - Last synced: 7 months ago - Pushed: 7 months ago

sanger-tol/blobtoolkit
Nextflow pipeline for BlobToolKit for Sanger ToL production suite
  • v1 .github/workflows/linting.yml

Size: 73.5 MB - Last synced: 5 months ago - Pushed: 5 months ago

nf-core/taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 11.9 MB - Last synced: 2 days ago - Pushed: 2 days ago

J-81/dp_tools
  • v1.1.0 .github/workflows/run_pytests.yml

Size: 1.89 MB - Last synced: 6 months ago - Pushed: 6 months ago

nf-core/crisprseq
A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 6.84 MB - Last synced: 2 days ago - Pushed: 2 days ago

nf-core/airrflow
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 8.19 MB - Last synced: 2 days ago - Pushed: 2 days ago

SMLMS/nfml
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 6.2 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

qbic-pipelines/root-tissue-analysis
Pipeline for pH analysis of A. thaliana root tissue
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 38 MB - Last synced: 3 months ago - Pushed: 3 months ago

ErikDanielsson/tools Fork of nf-core/tools
Python package with helper tools for the nf-core community.
  • v1 .github/workflows/create-lint-wf.yml
  • v1 .github/workflows/create-test-wf.yml
  • v1 .github/workflows/pytest.yml
  • v1 .github/workflows/rich-codex.yml
  • v1 .github/workflows/sync.yml

Size: 11.7 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

MillironX/taxprofiler Fork of nf-core/taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun metagenomic data
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 7 MB - Last synced: 12 months ago - Pushed: 12 months ago

matthdsm/nf-core-tools Fork of nf-core/tools
Python package with helper tools for the nf-core community.
  • v1 .github/workflows/create-lint-wf.yml
  • v1 .github/workflows/create-test-wf.yml
  • v1 .github/workflows/pytest.yml
  • v1 .github/workflows/rich-codex.yml
  • v1 .github/workflows/sync.yml

Size: 8.74 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

alnfedorov/rnaseq Fork of nf-core/rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 63.1 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

ewels/nf-core-rnaseq Fork of nf-core/rnaseq
See the main fork of this repository here >>>
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 63.9 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

MatthiasZepper/tools Fork of nf-core/tools
Python package with helper tools for the nf-core community.
  • v1 .github/workflows/create-lint-wf.yml
  • v1 .github/workflows/create-test-wf.yml
  • v1 .github/workflows/pytest.yml
  • v1 .github/workflows/rich-codex.yml
  • v1 .github/workflows/sync.yml

Size: 19.1 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

viash-io/website
  • v1.2.0 .github/workflows/gh-pages.yml

Size: 118 MB - Last synced: 9 days ago - Pushed: 9 days ago

sanger-tol/sequencecomposition
Nextflow pipeline to extract statistics from a genome about its sequence composition
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 2.65 MB - Last synced: 7 months ago - Pushed: 7 months ago

genomic-medicine-sweden/gmsmetapost
GMS Metagenomics post-classification
  • v1 .github/workflows/ci.yml

Size: 13.8 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

JoseEspinosa/nf-core-rnaseq Fork of nf-core/rnaseq
Main pipeline here:
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 63.5 MB - Last synced: 2 months ago - Pushed: 2 months ago

openproblems-bio/openproblems-v2
Formalizing and benchmarking open problems in single-cell genomics
  • v1.2.0 .github/workflows/integration-test.yml
  • v1.2.0 .github/workflows/release-build.yml

Size: 160 MB - Last synced: 3 days ago - Pushed: 3 days ago

nf-core/tools
Python package with helper tools for the nf-core community.
  • v1 .github/workflows/create-lint-wf.yml
  • v1 .github/workflows/create-test-wf.yml
  • v1 .github/workflows/pytest.yml
  • v1 .github/workflows/rich-codex.yml
  • v1 .github/workflows/sync.yml

Size: 19.6 MB - Last synced: 2 days ago - Pushed: 2 days ago

maxulysse/nf-core_sarek Fork of nf-core/sarek
Main repo:
  • v1.2.0 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 39.6 MB - Last synced: 27 days ago - Pushed: 28 days ago

nf-cmgg/germline
A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 8.53 MB - Last synced: 12 days ago - Pushed: 12 days ago

Arcadia-Science/hifi2genome
Assemble PacBio Hifi reads into a genome and perform QC stats
  • v1 .github/workflows/ci.yml

Size: 2.81 MB - Last synced: 9 months ago - Pushed: 9 months ago

nf-core/demultiplex
Demultiplexing pipeline for sequencing data
  • v1 .github/workflows/linting.yml

Size: 12.6 MB - Last synced: 2 days ago - Pushed: 2 days ago

tillenglert/quantms Fork of nf-core/quantms
Quantitative mass spectrometry workflow.
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 7.91 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

ClinicalGenomicsGBG/nf-core-raredisease Fork of nf-core/raredisease
Main pipeline here:
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 6.34 MB - Last synced: about 2 months ago - Pushed: 9 months ago

bjlang/nf-core-atacseq Fork of nf-core/atacseq
ATAC-seq peak-calling, QC and differential analysis pipeline
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 9.32 MB - Last synced: 29 days ago - Pushed: 29 days ago

dalmolingroup/bulkrna
Dalmolin Group's workflow for pre-processing, alignment and quantification of bulk RNA-seq data
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 2.29 MB - Last synced: 11 months ago - Pushed: 11 months ago

dicerna/fetchngs Fork of nf-core/fetchngs
Pipeline to fetch metadata and raw FastQ files from public and private databases
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 2.63 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

atrigila/nf-core-saliva
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 2.23 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

awh082834/Habu
Hybrid Assembly of Bacteria utilizing Unicycler
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 2.2 MB - Last synced: 11 months ago - Pushed: over 1 year ago

SystemsGenetics/EnTAPnf
Functional Annotation of Gene Lists
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 4.28 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

ashotmarg/partis_nfcore
Creating a demo nfcore pipeline
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 2.3 MB - Last synced: 7 months ago - Pushed: over 1 year ago

nextflow-io/patterns
A curated collection of Nextflow implementation patterns
  • v1 .github/workflows/test.yml

Size: 2.4 MB - Last synced: 6 months ago - Pushed: 6 months ago

nf-core/chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline.
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 15.3 MB - Last synced: 1 day ago - Pushed: 2 days ago

robomics/call_tad_cliques
Nextflow workflow to call TAD cliques
  • v1 .github/workflows/ci.yml

Size: 146 KB - Last synced: 8 months ago - Pushed: 8 months ago

nf-core/hlatyping
Precision HLA typing from next-generation sequencing data
  • v1 .github/workflows/ci.yml
  • v1 .github/workflows/linting.yml

Size: 39.3 MB - Last synced: 2 days ago - Pushed: 2 days ago

cmatKhan/alignercompare
Compare various aligners for IsoSeq assembled TX
  • v1 .github/workflows/ci.yml

Size: 4.96 MB - Last synced: about 1 year ago - Pushed: over 1 year ago