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Projects in Awesome Lists tagged with nextflow
A curated list of projects in awesome lists tagged with nextflow .
https://github.com/nextflow-io/nextflow
A DSL for data-driven computational pipelines
aws bioinformatics cloud dataflow docker groovy hello hpc nextflow pipeline pipeline-framework reproducible-research reproducible-science sge singularity singularity-containers slurm workflow-engine
Last synced: 17 Dec 2024
https://github.com/nf-core/sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
annotation bioinformatics cancer conda containers gatk4 genomics germline next-generation-sequencing nextflow nf-core pipeline pre-processing reproducible-research somatic target-panels variant-calling whole-exome-sequencing whole-genome-sequencing workflow
Last synced: 07 Nov 2024
https://github.com/bactopia/bactopia
A flexible pipeline for complete analysis of bacterial genomes
bacterial-genomes bioconda conda fastqs nextflow
Last synced: 13 Nov 2024
https://github.com/nextflow-io/patterns
A curated collection of Nextflow implementation patterns
Last synced: 13 Nov 2024
https://github.com/lynnlangit/gcp-for-bioinformatics
GCP for Bioinformatics Researchers
bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-researchers gcp genomics google google-batch nextflow
Last synced: 18 Dec 2024
https://github.com/nvuillam/npm-groovy-lint
Lint, format and auto-fix your Groovy / Jenkinsfile / Gradle files using command line
ci code-quality-analyzer codenarc gradle groovy groovy-language hacktoberfest jenkinsfile lint linter megalinter nextflow sarif sarif-report
Last synced: 19 Dec 2024
https://github.com/nf-core/chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline.
chip chip-seq chromatin-immunoprecipitation macs2 nextflow nf-core peak-calling pipeline workflow
Last synced: 09 Nov 2024
https://github.com/nf-core/nanoseq
Nanopore demultiplexing, QC and alignment pipeline
alignment demultiplexing nanopore nextflow nf-core pipeline qc workflow
Last synced: 13 Nov 2024
https://github.com/nf-core/atacseq
ATAC-seq peak-calling and QC analysis pipeline
atac-seq chromatin-accessibiity nextflow nf-core pipeline workflow
Last synced: 16 Nov 2024
https://github.com/lynnlangit/aws-for-bioinformatics
AWS for Bioinformatics Researchers
athena aws aws-batch awsbatch bioinformatics ec2 genomics nextflow sagemaker
Last synced: 15 Dec 2024
https://github.com/bastidanicolas/nextauth-prisma-stripe
How to integrate subscriptions into your Next.js project (/app). The tutorial utilizes Next.js (v13.4) with the /app directory structure, NextAuth v4 for authentication, Prisma for database management, and Stripe for payment processing.
auth authentication google-authentication mysql-database next-auth next-auth-adapter next-js nextflow nextjs nextjs13 nextjs14 prisma prisma-client route-protection stripe stripe-subscriptions subscription subscriptions-and-payments
Last synced: 21 Dec 2024
https://github.com/replikation/What_the_Phage
WtP: Phage identification via nextflow and docker or singularity
bioinformatics nextflow nextflow-pipelines phage-identification phage-sequences phages
Last synced: 20 Nov 2024
https://github.com/fmalmeida/bacannot
Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
annotation antimicrobial-genes-annotation barrnap genome-analysis genome-browser genomic-islands-prediction insertion-sequences ko-annotation methylation-annotation mobile-genetic-elements nextflow phigaro pipeline prophage-sequences-prediction prophages reproducible-research rgi rrna-prediction virulence-factor virulence-genes
Last synced: 13 Nov 2024
https://github.com/likelet/lncpipe
A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets
Last synced: 10 Nov 2024
https://github.com/nextflow-io/rnaseq-nf
A proof of concept of RNAseq pipeline
Last synced: 13 Nov 2024
https://github.com/nvuillam/vscode-groovy-lint
VSCode extension to lint , correct and format groovy and Jenkinsfile
code-quality-analyzer codenarc gradle groovy groovy-language jenkinsfile linter nextflow vscode vscode-extension
Last synced: 16 Dec 2024
https://github.com/lumc/pytest-workflow
Configure workflow/pipeline tests using yaml files.
cromwell miniwdl nextflow pipeline pytest pytest-plugin snakemake test testing wdl wdl-devtools workflow workflow-testing yaml
Last synced: 18 Dec 2024
https://github.com/nf-core/website
Code and files for the main nf-core website.
Last synced: 01 Nov 2024
https://github.com/mribeirodantas/nextflowsnippets
This repository hosts a large collection of Nextflow snippets
nextflow nextflow-language pipeline programming snippets workflow
Last synced: 04 Dec 2024
https://github.com/brwnj/covviz
Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata
coverage genomics-visualization nextflow
Last synced: 17 Nov 2024
https://github.com/augustdev/nf-shard
Nextflow runs monitoring and organisation UI
Last synced: 19 Dec 2024
https://github.com/nextflow-io/nf-validation
Params validation plugin for Nextflow pipelines
json-schema nextflow plugin samplesheet validation
Last synced: 13 Nov 2024
https://github.com/danrlu/nextflow_cheatsheet
Tips for Nextflow and cheatsheet for channel operation
Last synced: 14 Nov 2024
https://github.com/Gregor-Mendel-Institute/aradeepopsis
A versatile, fully open-source pipeline to extract phenotypic measurements from plant images
arabidopsis-thaliana deep-learning nextflow plant-phenotyping scikit-image semantic-segmentation tensorflow
Last synced: 14 Nov 2024
https://github.com/gregor-mendel-institute/aradeepopsis
A versatile, fully open-source pipeline to extract phenotypic measurements from plant images
arabidopsis-thaliana deep-learning nextflow plant-phenotyping scikit-image semantic-segmentation tensorflow
Last synced: 06 Nov 2024
https://github.com/midnighter/nextflow-gotchas
A collection of unexpected challenges and learnings with nextflow and nf-core.
gotcha nextflow nextflow-pipeline nextflow-process nextflow-workflow nf-core
Last synced: 09 Nov 2024
https://github.com/janeliascicomp/multifish
EASI-FISH analysis pipeline for spatial transcriptomics
easi-fish ibm-platform-lsf nextflow pipeline
Last synced: 16 Nov 2024
https://github.com/nextflow-io/nf-hack17-tutorial
Nextflow basic tutorial for newbie users
bioinformatics docker genomics nextflow singularity tutorial
Last synced: 13 Nov 2024
https://github.com/JaneliaSciComp/multifish
EASI-FISH analysis pipeline for spatial transcriptomics
easi-fish ibm-platform-lsf nextflow pipeline
Last synced: 08 Nov 2024
https://github.com/fmalmeida/ngs-preprocess
A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies
bax2bam bioinformatics illumina nanopack nextflow ngs ngs-preprocess pacbio pacbio-ccs pipeline porechop reproducible-research reproducible-science trimgalore workflow
Last synced: 13 Nov 2024
https://github.com/nextflow-io/vscode-language-nextflow
Nextflow language support for Visual Studio Editor
Last synced: 13 Nov 2024
https://github.com/cdcgov/tostadas
🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
azure bioinformatics conda docker genbank genetics liftoff metadata mpox ncbi nextflow nf-tower pipeline python rna-seq scicomp sequencing singularity sra vadr
Last synced: 16 Nov 2024
https://github.com/brwnj/idplot
compare sequences to a shared root reference sequence.
fasta nextflow plotly recombination sars-cov-2 virus
Last synced: 17 Nov 2024
https://github.com/nextflow-io/crg-course-nov16
Nextflow + Docker tutorial material
Last synced: 13 Nov 2024
https://github.com/biocorecrg/MOP2
Master of Pores 2
cdna docker nanopore nextflow pipeline rna rna-seq singularity
Last synced: 13 Nov 2024
https://github.com/nextflow-io/hyperopt
Nextflow pipeline for hyperparameter optimization of machine learning models
Last synced: 13 Nov 2024
https://github.com/nextflow-io/hello
Classic hello world script in Nextflow language
Last synced: 13 Nov 2024
https://github.com/robsyme/nf-repeatmasking
Nextflow workflow for automatic repeat detection, classification and masking
bioinformatics genomics nextflow transposable-elements
Last synced: 15 Oct 2024
https://github.com/sydney-informatics-hub/bioinformatics
A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.
bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts cancer genomics germline-variants indels metagenomics nextflow nextflow-pipelines ngs research-computing rnaseq snps somatic-variants sydney-informatics-hub transcriptomics variant-calling
Last synced: 21 Nov 2024
https://github.com/nextflow-io/rmghc-2018
Nextflow Workshop at Rocky Mountain Genomics HackCon 2018
containers genomics hackathon nextflow workflows
Last synced: 13 Nov 2024
https://github.com/mribeirodantas/nf-whisper
Proof-of-concept Nextflow pipeline to interact with OpenAI Whisper
docker nextflow pipeline speech-to-text transcription whisper
Last synced: 15 Oct 2024
https://github.com/vmikk/phylonext
A pipeline for phylogenetic diversity analysis of GBIF-mediated data
beta-diversity biodiverse docker endemism gbif nextflow phylodiversity phylogenetic-diversity r randomisations singularity
Last synced: 02 Dec 2024
https://github.com/bentsherman/tesseract
A tool for creating resource prediction models for scientific workflows
high-performance-computing machine-learning nextflow scientific-computing scientific-workflows
Last synced: 15 Oct 2024
https://github.com/truwl/capanno
cwl/wdl/sm/nf files, tool and workflow metadata, and input specifications.
Last synced: 23 Oct 2024
https://github.com/nextflow-io/atom-language-nextflow
Nextflow syntax highlighter for Atom editor
Last synced: 13 Nov 2024
https://github.com/proycon/nederlab-pipeline
Linguistic enrichment pipeline for historical dutch, as used in the Nederlab project
dutch historical-dutch historical-linguistics natural-language-processing nederlab nextflow nlp workflow
Last synced: 19 Oct 2024
https://github.com/nextflow-io/language-server
The Nextflow language server
language-server-protocol nextflow
Last synced: 13 Nov 2024
https://github.com/seandavi/nextflow_on_jupyter
A lightweight introduction to NextFlow, a workflow description language and engine for (mainly) bioinformatics workflows. Leverages notebooks for easy teaching.
bioinformatics jupyter nextflow notebook tutorial
Last synced: 05 Nov 2024
https://github.com/nextflow-io/gccbosc18-training
Documentation for Nextflow training at GCC/BOSC 2018
Last synced: 13 Nov 2024
https://github.com/vmikk/nextits
A pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio
eukaryotes fungi internal-transcribed-spacer its metabarcoding nextflow pacbio pipeline
Last synced: 02 Dec 2024
https://github.com/jagedn/nf-plugin-template
Unoficial template for Nextflow Plugins
groovy groovy-language nextflow nextflow-plugin
Last synced: 13 Nov 2024
https://github.com/maxulysse/compile-latex
Simple beamer/latex compiler using Nextflow, provided with Docker container
beamer-compiler container docker latex nextflow
Last synced: 13 Nov 2024
https://github.com/lieberinstitute/speaqeasy
SPEAQeasy: portable LIBD RNA-seq pipeline using Nextflow. Check http://research.libd.org/SPEAQeasy-example/ for an example on how to use this pipeline and analyze the resulting output files.
hisat2 nextflow pipeline rna-seq-pipeline rnaseq rstats speaqeasy
Last synced: 30 Nov 2024
https://github.com/sydney-informatics-hub/germline-structuralv-nf
Germline structural variant calling pipeline for short read WGS datasets
annotsv australian-biocommons bam bioinformatics dsl2 genomics germline-variant-calling manta nextflow ngs pipeline smoove structural-variants survivor tiddit workflow
Last synced: 21 Nov 2024
https://github.com/rennelab/cnr-flow
CUT&RUN-Flow, A Nextflow pipeline for QC, tag trimming, normalization, and peak calling for data from CUT&RUN experiments.
chip-seq-pipelines cutandrun cutandrun-seq cutrun genomics nextflow peak-calling
Last synced: 08 Nov 2024
https://github.com/stracquadaniolab/cookiecutter-workflow-nf
A standardized directory structure to build workflows using Nextflow.
Last synced: 13 Nov 2024
https://github.com/lieberinstitute/speaqeasyworkshop2020
EuroBioc2020 SPEAQeasy workshop https://eurobioc2020.bioconductor.org by Nick Eagles and Josh Stolz. For more information about SPEAQeasy check http://research.libd.org/SPEAQeasy/. For an example on how to use this RNA-seq processing pipeline and analyze the output files check http://research.libd.org/SPEAQeasy-example/.
bioconductor limma nextflow nextflow-pipelines rnaseq-pipeline rstats speaqeasy
Last synced: 30 Nov 2024
https://github.com/inab/tcga_benchmarking_workflow
benchmarking nextflow openebench tcga
Last synced: 10 Nov 2024
https://github.com/nextflow-io/nf-weblog
Implement weblog plugin for Nextflow
Last synced: 13 Nov 2024
https://github.com/nschan/nf-genomeassembly
Nextflow pipeline to assemble genomes from long reads.
annotation arabidopsis arabidopsis-thaliana genome genome-assembly genome-sequencing hifi long-read-sequencing long-reads nanopore nextflow nextflow-pipeline nextflow-pipelines oxford-nanopore pacbio pacbio-hifi-sequencing-reads scaffolding
Last synced: 06 Nov 2024
https://github.com/midnighter/nf-core-adr
Structurizr documentation of nf-core
architecture-decision-records nextflow nf-core structurizr
Last synced: 09 Nov 2024
https://github.com/jbris/nextflow-graph-machine-learning
A Nextflow pipeline demonstrating how to train graph neural networks for gene regulatory network reconstruction using DREAM5 data.
deep-learning docker docker-compose dream5 gene-regulatory-network gene-regulatory-network-inference gene-regulatory-networks graph-neural-network graph-neural-networks graphsage machine-learning minio mlflow mlops nextflow nextflow-pipeline nextflow-pipelines variational-autoencoder variational-inference
Last synced: 13 Nov 2024
https://github.com/brainstorm/bwa-nextflow-benchmark
Small test to compare AWS and HPC on a very simple workflow
aws bioinformatics-pipeline bwa-mem hpc kubernetes nextflow samtools
Last synced: 15 Dec 2024
https://github.com/j-e-j-s/aars-pipeline
A Scalable Pipeline for Discovery of aaRS Mutants to Aid in Genetic Code Expansion.
bioengineering bioinformatics biology computational-biology nextflow pipeline python synthetic-biology
Last synced: 16 Dec 2024
https://github.com/sydney-informatics-hub/hpc_usage_reports
Scripts to pull resource usage data from job logs for Artemis and Gadi into tab-delimited format and to report queue time from job history
artemis gadi hpc nci-gadi nextflow nf-core usyd-artemis
Last synced: 21 Nov 2024
https://github.com/midnighter/cookiecutter-nf-plugin
A cookiecutter template for creating nextflow plugins.
cookiecutter cookiecutter-nextflow nextflow nextflow-plugin plugin template
Last synced: 09 Nov 2024
https://github.com/azavea/pipeline-playground
A repository with usage examples of various pipeline and workflow orchestration tools
aws aws-pipeline nextflow nextflow-pipelines step-functions
Last synced: 10 Nov 2024
https://github.com/t-neumann/nextflow-ngs
Generic Nextflow processes for next-generation sequencing data analysis
Last synced: 10 Nov 2024
https://github.com/janeliascicomp/nf-demos
Nextflow Demo Pipelines for Image Processing
Last synced: 08 Nov 2024
https://github.com/gauravcodepro/nextflow-pacbiohifi
a nextflow pacbiohifi for the genome assembly from the pacbiohifi
bioinformatics nextflow nextflow-language nextflow-pipeline nextflow-process pacbio-data pacbiohifi
Last synced: 09 Nov 2024
https://github.com/midnighter/nf-join-map
Demonstrate problems with merging channels using a map as the key to merge by.
Last synced: 09 Nov 2024
https://github.com/abhi18av/nextflow_grid_search
data-science-workflows h2oai machine-learning-algorithms nextflow
Last synced: 09 Nov 2024
https://github.com/lieberinstitute/biocmap
Our typical analysis steps for WGBS data, starting from FASTQ reads and ending with the construction of bsseq objects. Created using nextflow
Last synced: 30 Nov 2024
https://github.com/rbpisupati/nf-haplocaller
Nextflow pipeline for GATK best practices (HaplotypeCaller)
awesome-nextflow gatk haplotypecaller nextflow snp-calling
Last synced: 06 Nov 2024
https://github.com/ankushkgupta2/databricks-poc
:computer: :bar_chart: Proof of Concept (POC) Using Azure Databricks for Automated & Real-Time ETL, Generation of Visualizations, and Pipeline Integration for Various Pathogens
api azure backend blob clarity-lims database databricks dbfs elims elt etl graph-database json livetables metadata mpxv nextflow parquet poc yaml
Last synced: 08 Nov 2024
https://github.com/stracquadaniolab/cubseq-nf
CUBseq analyses codon usage bias from RNA-seq data, producing robust CUB estimates that account for variants transcriptome-wide and in highly expressed genes.
codon-bias codon-optimization codon-usage nextflow rnaseq transcriptomics
Last synced: 13 Nov 2024
https://github.com/jbris/nextflow-tutorials
Working through NextFlow tutorials. See https://github.com/nextflow-io/training
dag directed-acyclic-graph docker groovy groovy-language nextflow nextflow-dsl2 nextflow-lang nextflow-language nextflow-pipeline nextflow-pipelines nextflow-process nextflow-training nextflow-tutorial nextflow-tutorials nextflow-workflow pipeline pipelines workflow workflows
Last synced: 13 Nov 2024
https://github.com/cdcgov/bpertussis-ciwgs
Culture-Independent Whole Genome Sequencing (CIWGS) Read Filter Pipeline 🧪🧬🖥️
bioinformatics genomic-surveillance nextflow pertussis wgs
Last synced: 08 Nov 2024
https://github.com/edn-es/nf-plugin-template
An unofficial template to build Nextflow Plugins
groovy nextflow nextflow-plugin
Last synced: 19 Nov 2024
https://github.com/cometsong/atac_seq_nxf
ATAC_Seq Analysis Pipeline using Nextflow framework.
atac-seq bioinformatics nextflow pipeline
Last synced: 20 Nov 2024
https://github.com/anfederico/generative-nf
Dynamic Hierarchical Workflows via Generative Nextflow
Last synced: 30 Nov 2024
https://github.com/zsteve/nf-atac
ATAC-seq pipeline written in Nextflow
atac-seq bioinformatics epigenomics nextflow ngs pipeline
Last synced: 09 Dec 2024
https://github.com/bentsherman/nextflow-palmetto-demo
Creating and running Nextflow pipelines on Clemson's Palmetto cluster
Last synced: 04 Dec 2024
https://github.com/gp201/freyja_pathogen_workflow_alpha
Used to produce the barcodes for Freyja.
Last synced: 12 Oct 2024
