nextflow-pipeline | Topic | Ecosyste.ms: Repos

Topic: "nextflow-pipeline"

biocorecrg/master_of_pores

Nextflow pipeline for analysis of direct RNA Nanopore reads

Language: Nextflow - Size: 448 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 101 - Forks: 17

Midnighter/nextflow-gotchas

A collection of unexpected challenges and learnings with nextflow and nf-core.

Language: Shell - Size: 707 KB - Last synced at: 3 days ago - Pushed at: over 1 year ago - Stars: 36 - Forks: 9

PalMuc/TransPi

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

Language: Nextflow - Size: 48.6 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 24 - Forks: 14

mahesh-panchal/nf-cascade

A proof of concept daisy-chaining Nextflow workflows

Language: Nextflow - Size: 44.9 KB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 22 - Forks: 5

bzhanglab/neoflow

NeoFlow: a proteogenomics pipeline for neoantigen discovery

Language: Nextflow - Size: 4.01 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 22 - Forks: 12

nf-cmgg/structural

A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads

Language: Nextflow - Size: 5.37 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 19 - Forks: 2

guigolab/geneidx

Nextflow pipeline for genome annotation of protein-coding genes

Language: Nextflow - Size: 202 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 15 - Forks: 2

TORCH-Consortium/MAGMA

A pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis with a focus on clinical decision making as well as research

Language: Nextflow - Size: 36.3 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 13 - Forks: 3

cellgeni/cellatac

Sanger Cellular Genetics single-cell ATAC-seq pipeline.

Language: Nextflow - Size: 207 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 11 - Forks: 5

INMEGEN/Pipelines_Inmegen

Flujos de trabajos desarrollados y automatizados en el Intituto Nacional de Medicina Genómica para el procesamiento de datos genómicos y transcriptómicos.

Language: Nextflow - Size: 7.37 MB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 9 - Forks: 0

DIncalciLab/samurai

A bioinformatics best-practice analysis pipeline for the analysis of shallow whole genome sequencing (sWGS) data for the identification of copy number alterations (CNAs).

Language: Nextflow - Size: 3.93 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 8 - Forks: 0

CDCgov/MIRA-NF

Language: Nextflow - Size: 12.1 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 7 - Forks: 6

jhayer/baargin

Bacterial Assembly and Antimicrobial Resistance Genes In NextFlow

Language: Nextflow - Size: 15.4 MB - Last synced at: 1 day ago - Pushed at: 6 months ago - Stars: 7 - Forks: 0

AustralianBioCommons/Nextflow_DSL2_template 📦

Template for creating Nextflow DSL2 pipelines

Size: 77.1 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 6 - Forks: 2

JBris/nextflow-graph-machine-learning

A Nextflow pipeline demonstrating how to train graph neural networks for gene regulatory network reconstruction using DREAM5 data.

Language: Python - Size: 5.69 MB - Last synced at: 15 days ago - Pushed at: 5 months ago - Stars: 5 - Forks: 1

icaromsc/nf-core-phiflow

Language: Nextflow - Size: 2.26 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 0

kirilenkobm/py_nf

Python library to execute batches of jobs using nextflow.

Language: Python - Size: 49.8 KB - Last synced at: 9 months ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 1

mriffle/nf-skyline-dia-ms

Nextflow workflow for performing DIA proteomics

Language: Nextflow - Size: 365 KB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 4 - Forks: 3

BirgitRijvers/EMC-MetaMicrobes

Nextflow pipeline to detect and classify microbial reads in sequencing data from human samples.

Language: Nextflow - Size: 10.4 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 4 - Forks: 2

salvadorlab/mbovpan

Mbovpan is a nextflow bioinformatic pipeline for Mycobacterium bovis pangenome analysis. The goal of Mbovpan is to help researchers to study the M. bovis pangenome in an automatic and easy way.

Language: Nextflow - Size: 389 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 4 - Forks: 0

eipm/hello-mess-nf

A Nextflow pipeline to experiment with DSL2 + Zero Mess

Language: Nextflow - Size: 81.1 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 4 - Forks: 1

phipsonlab/NextClone

Nextflow pipeline for extracting and counting clonal barcodes

Language: Python - Size: 1.14 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 1

BCCDC-PHL/dragonflye-nf

Nextflow wrapper for the dragonflye assembler, with additional QC

Language: Nextflow - Size: 600 KB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1

angelovangel/nxf-bcl

A simple nextflow pipeline for Illumina run metrics (InterOp) and generation of fastq files (bcl2fastq)

Language: Nextflow - Size: 42 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 3

amchakra/tosca

Nextflow analysis pipeline for hiCLIP and proximity ligation sequencing data

Language: Nextflow - Size: 406 KB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 3 - Forks: 3

renatosantos98/ont-benchmark

Supporting data for the publication "Investigating the performance of Oxford Nanopore long-read sequencing with respect to Illumina microarrays and short-read sequencing"

Language: Jupyter Notebook - Size: 156 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 3 - Forks: 0

WEHI-ResearchComputing/nf-alphafold

Language: Nextflow - Size: 696 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 0

nschan/nf-genomeassembly

Nextflow pipeline to assemble genomes from long reads.

Language: Nextflow - Size: 1000 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 0

asadprodhan/sangerFlow

A bioinformatics pipeline that automates the Sanger amplicon sequencing data analysis of thousands of samples in parallel.

Language: Nextflow - Size: 1.16 MB - Last synced at: 12 days ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 0

bguo068/snp_call_nf

Nextflow pipeline for plasmodium SNP calling

Language: Nextflow - Size: 105 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 3 - Forks: 3

Sydney-Informatics-Hub/template-nf

A straightforward Nextflow workflow template generator.

Size: 391 KB - Last synced at: about 1 month ago - Pushed at: 7 months ago - Stars: 3 - Forks: 0

biosustain/dsp_nf-metagenomics

Shotgun metagenomics pipeline to process microbiome samples

Language: Shell - Size: 200 KB - Last synced at: 18 days ago - Pushed at: 11 months ago - Stars: 3 - Forks: 0

BU-ISCIII/panelLowFreq-nf

This is a nextflow pipeline for variant calling of low frequency variants in panel/WES high-throughput data.

Language: Nextflow - Size: 328 KB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 3 - Forks: 0

JLP-BioInf/rnaCrosslinkNF

Pre-processing pipeline for RNA crosslinking and High throughput sequencing data.

Language: R - Size: 38.8 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0

vonMeyennLab/nf_cutntag

A Nextflow pipeline to perform quality control, alignment, and feature coverage of CUT&Tag sequencing data.

Language: Nextflow - Size: 58.6 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 2 - Forks: 0

joanmarticarreras/VANIR

NextFlow pipeline for Virus Variant calling and de novo Assembly of Nanopore and Illumina Reads

Language: HTML - Size: 6.09 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

bixBeta/nextflow

nextflow RNAseq pipeline for GG02

Language: Nextflow - Size: 2.89 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 1 - Forks: 1

uclanelsonlab/nl-rna-seq_wf

RNA-seq for rare diseases pipeline using nextflow

Language: Nextflow - Size: 12.9 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 1 - Forks: 0

proteomicsunitcrg/atlas

Single-file quality control prototyping pipeline for diverse mass spectrometry workflows.

Language: Nextflow - Size: 191 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 1 - Forks: 0

vonMeyennLab/nf_peakcalling

A Nextflow pipeline to perform peak calling of ChIP-seq, ATAC-seq or CUT&Tag sequencing data.

Language: Nextflow - Size: 10.7 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

plantinformatics/shortbread2

Shortbread2 is a bioinformatics pipeline for identifying single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) from High-Throughput Next Generation Sequencing (NGS) data.

Language: Perl - Size: 819 MB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

ghga-de/nf-platypusindelcalling

This page is reserved for NextFlow based Indell Calling Workflow (with Platypus) from DKFZ

Language: Python - Size: 119 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

a-hr/lexogen_pipeline

Nextflow pipeline used to count expression on target-RNA experiments.

Language: Python - Size: 57.6 KB - Last synced at: 10 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

bguo068/posseleff_simulations

Nextflow pipeline to assess the impact of positive selection on Identity by Descent (IBD)-based inferences, utilizing population genetic simulations and true IBD inferences.

Language: Python - Size: 66.7 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

IceGreb/MetaSA-Scan

Metagenomic Sequence Analysis domain scanner

Language: Nextflow - Size: 1.3 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

bce99/m6A-RNA-Modification-Prediction

:dna: A prediction pipeline of m6A RNA modifications on all SG-NEx direct RNA-Seq samples using Nextflow and FeedForward Neural Network

Language: Jupyter Notebook - Size: 17.7 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

JBris/nextflow-tutorials

Working through NextFlow tutorials. See https://github.com/nextflow-io/training

Language: HTML - Size: 2.57 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

duncanberger/nxf-BATQual

Bacterial genome assembly, annotation and typing pipeline.

Language: Python - Size: 321 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

jadedavis5/combo-seq

Analyse combined miRNA/mRNA reads produced using Combo-Seq kit

Language: Shell - Size: 139 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

Giulia-Calia/PLANTOGEN-A

PLANTOGEN-A, an automated genome assembly pipeline designed to assemble symbiont microorganisms genome from Oxford Nanopore (ONT) data.

Language: Common Workflow Language - Size: 47.9 KB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

jlboat/NextflowScripts

Misc. Nextflow scripts

Language: Nextflow - Size: 7.81 KB - Last synced at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 1 - Forks: 0

Kincekara/nf-BIRD

Bacterial Identification and Antimicrobial Resistance

Language: Nextflow - Size: 50.8 KB - Last synced at: about 3 hours ago - Pushed at: about 4 hours ago - Stars: 0 - Forks: 0

Elembio/bases2fastq-nf

Bases2fastq-nf is a bioinformatics pipeline used to demultiplex the raw data produced by the Element AVITI™ System using the Bases2Fastq Software.

Language: Nextflow - Size: 53.5 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 0 - Forks: 2

nmendozam/kir-mapper

Nextflow pipeline for kir-mapper map

Language: Nextflow - Size: 3.91 KB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 0 - Forks: 0

catg-umag/ont-basecalling-demultiplexing

Nextflow pipeline for basecalling / demultiplexing ONT data, using Dorado

Language: Nextflow - Size: 71.3 KB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 0 - Forks: 2

connor122721/nf-eqtls

Nextflow pipeline for disease eQTL mapping and follow up analyses

Language: R - Size: 12 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 0 - Forks: 0

phesketh-igtp/HUGTiP-HIV-1.nf

Nextflow workflow for the detection and lineage typing of HIV-1 genomes. This worklow is an updated and modified version of QuasiFlow

Language: Nextflow - Size: 99.8 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

ayoraind/floria_nextflow

This pipeline uses Floria for strain resolution. It also uses floria-strainer to strain out genomes from floria's output

Language: Python - Size: 17.6 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

cnr-ibba/nf-resequencing-mem

Nextflow resequencing pipeline with bwa-mem and freebayes

Language: Nextflow - Size: 2.66 MB - Last synced at: 11 days ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

cnr-ibba/nf-neestimator

A nextflow pipeline for Current Effective Population Size (Ne) calculations with bootstrapping

Language: Nextflow - Size: 159 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

sguizard/nf-mixcr

A nextflow pipeline for TCR repertoire building with MiXCR

Language: Nextflow - Size: 7.01 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

phesketh-igtp/RutiSeq-nf

RutiSeq-nf is intended for the classification, clustering and SNP barcoding of Mycobacterium tuberculosis genomes for outbreak surveillance.

Language: Nextflow - Size: 77.8 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

vonMeyennLab/nf_qc

A Nextflow pipeline to perform quality control of sequencing data.

Language: Nextflow - Size: 31.3 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

vonMeyennLab/nf_methylseq

A Nextflow pipeline to align and quantify Methylation (Bisulfite) sequencing data.

Language: Nextflow - Size: 93.8 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

nexomis/compress_fq

Workflow to compress a whole directory from fastq files to spring with sequence check.

Language: Nextflow - Size: 101 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

nexomis/rna-preprocessing

Estimate the expression level of features (genes or transcripts) and perform the associated QC. Starting from cleaned reads and one pre-built reference database in standard format (cf. Readme.md).

Language: Nextflow - Size: 56.6 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

Mirocow/nextflow-example-1

Nextflow + Wave+ Kubernetes

Language: Nextflow - Size: 12.7 KB - Last synced at: 18 days ago - Pushed at: 2 months ago - Stars: 0 - Forks: 1

sanger-bentley-group/GBS-Typer-sanger-nf

GBS Typer Pipeline in Nextflow

Language: Python - Size: 162 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 1

WEHI-ResearchComputing/nf-malaria-variant-analysis

Language: R - Size: 53 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 1

nexomis/viral-assembly

Assemble the viral genome and perform the associated quality control (QC). Start with raw reads and one pre-built reference database in standard format (see README.md).

Language: Nextflow - Size: 189 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

vonMeyennLab/nf_rnaseq

A Nextflow pipeline to perform quality control, alignment, and quantification of RNA sequencing data.

Language: Nextflow - Size: 40 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

Rendrick27/MethanoReplica

High Throughput Sequencing at your fingertips

Language: HTML - Size: 682 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

The repository contains a comprehensive pipeline for genome assembly and quality assessment, designed for genomic data analysis. It integrates various bioinformatics tools for accurate genome assembly.

Language: HTML - Size: 79 MB - Last synced at: 7 days ago - Pushed at: 10 months ago - Stars: 0 - Forks: 1

biosustain/dsp_nf-msdap

Nextflow pipeline for MS-DAP, a downstream pipeline to generate statistical reports for MS data

Language: R - Size: 165 KB - Last synced at: 18 days ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

nexomis/hannot

nextflow pipeline for annotation using homology

Language: Nextflow - Size: 28.3 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

nexomis/viral_comp

Language: Python - Size: 35.2 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

jeffe107/MAGFlow

Workflow for MAG quality assessment and taxonomical annotation.

Language: Nextflow - Size: 2.22 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

Midnighter/metanetx-nf

A Nextflow pipeline for extracting, transforming, augmenting, and loading the MetaNetX contents into a SQL database.

Language: Nextflow - Size: 48.8 KB - Last synced at: about 2 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

paq88/Variant_Calling_Nextflow_pipeline

Pipeline for SNP Calling Created in Nextflow management system for purposesof testing the advantages of managed systems vs native applications in variant calling. The paper created and published one day is titled "NextFlow vs. plain Bash: Different Approaches to the Parallelisation of SNP Calling from the Whole Genome Sequence Data"

Language: Nextflow - Size: 11.7 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

sufyazi/tfbs-variant-calling-nf

Repository detailing a Nextflow pipeline to run mpileup variant callling on TF footprints.

Language: HTML - Size: 21.7 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

michalbukowski/rnaseq-pipeline-2

Simple Nextflow RNA-Seq pipeline

Language: Nextflow - Size: 871 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

tpatmd/STARS

Species-level Taxonomic Abundance from 16S rRNA Sequencing (STARS)

Language: Nextflow - Size: 1.95 KB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

MJBioInfo/nextflow-draft

In this repository , I explained how we can implement Nextflow workflow and extend to AWS batch integration

Language: Nextflow - Size: 2.76 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

tpatmd/amplimap-nf

A bioinformatic pipeline for aligning amplicon reads to a DNA database based on Nextflow

Language: Nextflow - Size: 129 KB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

cnr-ibba/nf-treemix

A nextflow pipeline which executes treemix on a population of interest

Language: Nextflow - Size: 111 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

jos4uke/viticall_nf Fork of grapediadb/workflows

Variant calling nextflow pipeline for Grapedia " Tinkering with GRAPEDIA Training School: a modern take on grapevine data analysis" (DATE: 26-28 June 2023 VENUE: FEM | Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Trento, Italy)

Language: Nextflow - Size: 3.91 KB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 2