Github nf-core

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August undefined, 2024

Webnf-core workflows follow a set of best practices and standardized conventions. nf-core workflows start from a common template and follow the same structure. Although you won’t need to edit code in the workflow project directory, having a basic understanding of the project structure will help you understand how to configure its execution and ... Webnfcore/ampliseq is a bioinformatics analysis pipeline used for amplicon sequencing, supporting denoising of any amplicon and, currently, taxonomic assignment of 16S, ITS, CO1 and 18S amplicons. Supported is paired-end Illumina or single-end Illumina, PacBio and IonTorrent data.

GitHub - nf-core/ampliseq: Amplicon sequencing analysis …

WebDec 16, 2024 · nf-core/methylseq is a bioinformatics analysis pipeline used for Methylation (Bisulfite) sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results. WebIntroduction. nf-core/raredisease is a bioinformatics best-practice analysis pipeline for calling and scoring variants from WGS/WES data of rare disease patients. This pipeline is heavily inspired by MIP. The pipeline is built … geology museum shop

nf-core workflows series - Introduction to nf-core

WebTools docs are built using GitHub Actions on the nf-core/tools repo using Sphinx. These actions sync the built HTML files via FTP. GitHub web hooks. There is a GitHub web hook at the nf-core organisation level which triggers the pipeline update script whenever a repo is created, or has a release etc. This pings the deploy_pipelines.php script. WebWelcome to @nf-core! @nf-core is a community effort to collect a curated set of analysis pipelines built using Nextflow ( @nextflow-io ). Here's how to get started: See available … Test data to be used for automated testing with the nf-core pipelines - Issues · nf … [nf-core/rnaseq#764] - Test fails when using GCP due to missing tools in the basic … Introduction. nf-core is a collection of high quality Nextflow pipelines. This … WebDec 19, 2024 · nf-core/tools can also be installed from PyPI using pip as follows: pip install nf-core Docker image There is a docker image that you can use to run nf-core/tools that has all of the requirements packaged (including Nextflow) and so should work out of the box. It is called nfcore/tools (NB: no hyphen!) chris suhar

GitHub - nf-core/test-datasets: Test data to be used for …

GitHub - nf-core/chipseq: ChIP-seq peak-calling, QC and …

WebNov 25, 2024 · The principle for nf-core test data is as small as possible, as large as necessary. Please see the guidelines for more detailed information. Always ask for guidance on the nf-core slack before adding new test data. Documentation. nf-core/test-datasets comes with documentation in the docs/ directory: Add a new test dataset; Use an … Webnf-core/mag is a bioinformatics best-practise analysis pipeline for assembly, binning and annotation of metagenomes. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute … geology museum rapid cityWebcircdna Public. Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells. genomics nextflow dna circular nf-core ecdna circle-seq. Python MIT 9 12 1 1 Updated 4 days ago. geology names for boys

"Webnf-core workflows follow a set of best practices and standardized conventions. nf-core workflows start from a common template and follow the same structure. Although you … " - Github nf-core

Github nf-core

WebNov 30, 2024 · nfcore/atacseq is a bioinformatics analysis pipeline used for ATAC-seq data. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. Web[nf-core/rnaseq#764] - Test fails when using GCP due to missing tools in the basic biocontainer; Updated pipeline template to nf-core/tools 2.4.1; Software dependencies. Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to ...

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WebDec 24, 2011 · A tool to tunnel TCP over HTTP, written in Go. Go 222 44. goto Public. A URL shortening service. JavaScript 213 35. goplayer Public. A web-based music player. HTML 154 45. webfront Public. WebMar 29, 2024 · nf-core/spinningjenny is a bioinformatics best-practice analysis pipeline for simulating the first industrial revolution using Agent Based Models. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner.

Webnf-core/viralrecon is a bioinformatics analysis pipeline used to perform assembly and intra-host/low-frequency variant calling for viral samples. The pipeline supports both Illumina and Nanopore sequencing data. WebOct 24, 2024 · Introduction. nf-core/hgtseq is a bioinformatics best-practice analysis pipeline built to investigate horizontal gene transfer from NGS data. The pipeline uses metagenomic classification of paired-read alignments against a reference genome to identify the presence of non-host microbial sequences within read pairs, and to infer potential ...

Webnf-core workflows use GitHub releases to tag stable versions of the code and software, making workflow runs totally reproducible. Packaged software. Pipeline dependencies … WebJun 23, 2024 · nf-core/rnavar is a bioinformatics best-practice analysis pipeline for GATK4 RNA variant calling. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a …

WebBytesize: nf-core/HackMD and reveal.js. HackMD.io is an open source, collaborative Markdown editor, which allows people to share, comment, and collaborate on documents. At nf-core we use HackMD extensively during hackathons and for notekeeping. This week, Maxime Garcia ( @maxulysse) will show us how to create Presentation Slides on …

Webnfcore/nanoseq is a bioinformatics analysis pipeline for Nanopore DNA/RNA sequencing data that can be used to perform basecalling, demultiplexing, QC, alignment, and downstream analysis. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. geology museums near meWebOct 24, 2024 · nf-core/smrnaseq is a bioinformatics best-practice analysis pipeline for Small RNA-Seq Best Practice Analysis Pipeline. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. geology museums united statesWebnf-core/rnafusion is a bioinformatics best-practice analysis pipeline for RNA sequencing analysis pipeline with curated list of tools for detecting and visualizing fusion genes. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. geology museum rapid city sdWebOct 3, 2024 · nfcore/chipseq is a bioinformatics analysis pipeline used for Chromatin ImmunopreciPitation sequencing (ChIP-seq) data. On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. chris suh boardWebA repository for hosting Nextflow configuration files containing custom parameters required to run nf-core pipelines at different Institutions. Table of contents Using an existing config Configuration and parameters Offline usage Adding a new config Testing Documentation Uploading to nf-core/configs Adding a new pipeline-specific config geology news articles 2021WebAug 25, 2024 · Introduction. nf-core/scflow is a bioinformatics pipeline for scalable, reproducible, best-practice analyses of single-cell/nuclei RNA-sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. Full case/control sc/sn-RNAseq analyses can be orchestrated ... chris suh emoryWebnf-core workflows use GitHub releases to tag stable versions of the code and software, making workflow runs totally reproducible. Packaged software. Pipeline dependencies are automatically downloaded and handled using Docker, Singularity, Conda, or other software management tools. There is no need for any software installations. chris suhar md