UPDATED: April 16, 2024 nf-core is a community effort to collect a curated set of analysis pipelines built using Nextflow. This post will walk you through running the nf-core RNA-Seq workflow. The pipeline uses the STAR aligner by default, and quantifies data using Salmon, providing gene/transcript counts and extensive quality Read more…
This is an updated version of the variant calling pipeline post published in 2016 (link). This updated version employs GATK4 and is available as a containerized Nextflow script on GitHub. Identifying genomic variants, including single nucleotide polymorphisms (SNPs) and DNA insertions and deletions (indels), from next generation sequencing data is Read more…
In this article I’ll go over three Nextflow patterns I frequently use to make development of Nextflow data processing pipelines easier and faster. I use each of these in most of my workflows, so they really come in handy. I am assuming here that you know what processes, channels, strings, Read more…