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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)

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VITI-CALL NextFlow pipeline

An open-source analysis pipeline to detect variants from whole genome or targeted sequencing

Introduction

VITI-CALL Nextflow pipeline is a workflow designed to detect variants on whole genome or targeted sequencing data, designed to work on Vitis genome. 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. It was initially developped on snakemake workflow engine for the Vitis 4k project (Sophie Blanc, Camille Rustenholz et al., INRAE, 2020-2023). it is a complete rewrite using Nextflow DSL2 of this pipeline, using one container per process which makes it easier to maintain and update dependencies.

todo: add a workflow image

From workflow template

Give a general description of the workflow, the instructions on how to run it, how to build the docker images starting from Dockerfiles (if necessary), what are the parameters (meaning, permitted values, etc.) and the expected output.

  • main.nf file should contains the main Nexflow workflow
  • modules directory should contains all the Nextflow files (one per module / process)
  • nextflow.config file should contains all the directives about which docker image to use per module / process as well as number of CPUs and RAM
  • dockerfiles directory should contains all the Dockerfile needed to build Docker images in case the image is not already present and downloadable from BIOCONDA (https://bioconda.github.io/) or DockerHUB (https://hub.docker.com/)

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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)

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