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nextflow-gotchas

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

nextflow_training

Code for Nextflow trau

nextflow_tutorial

nextflow_varcal

Nextflow Tutorial - Variant Calling Edition

nf-co.re

Code and files for the main nf-core website.

nf-file-utils

Query files for their type and compression state.

nf-test

Simple test framework for Nextflow pipelines

nf-test-examples

A nf-test getting-started guide.

nfcamp-tutorial

A tutorial for DLS-2 migration

patterns

A curated collection of Nextflow implementation patterns

project_template

An example of how to organize files for a research project to increase reproducibility

ps2_geotif

r-scripts

reach_pubmed

readmapping

Nextflow readmapping pipeline, part of the Tree of Life production suite.

reproduce_me

reproducible-research

A demonstration of how to work reproducibly using version control, containers, and a workflow manager.

reproducible-research-with-r

A short course at the Institute of Medicine

reproducible_research_bioinformatics

rstudio-verse

container based on rocker rstudio verse for CyVerse VICE

sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

snakemake-class

Class materials for the NIH HPC snakemake class

snakemake-vice

repo for Snakemake-VICE webinar 2020

snakemake_examples

snakemake_irods

snakemake_pysradb

terraform-aws-teaching

terraform scripts to start teaching instance

testpipeline

A small example pipeline used to test new nf-core infrastructure and common code.

tick_surveillance

Bioinformatics pipeline for analysis of amplicon sequencing of tick-associated microbes

training

Nextflow training material