# Research Object Crate for sanger-tol/insdcdownload v1.0.1 - Hefty mûmakil

Original URL: https://workflowhub.eu/workflows/666/ro_crate?version=1

# ![sanger-tol/ensemblgenedownload](docs/images/sanger-tol-ensemblgenedownload_logo.png) [![GitHub Actions CI Status](https://github.com/sanger-tol/ensemblgenedownload/workflows/nf-core%20CI/badge.svg)](https://github.com/sanger-tol/ensemblgenedownload/actions?query=workflow%3A%22nf-core+CI%22) [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7183206-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7183206) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) [![Get help on Slack](http://img.shields.io/badge/slack-SangerTreeofLife%20%23pipelines-4A154B?labelColor=000000&logo=slack)](https://SangerTreeofLife.slack.com/channels/pipelines) [![Follow on Twitter](http://img.shields.io/badge/twitter-%40sangertol-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/sangertol) [![Watch on YouTube](http://img.shields.io/badge/youtube-tree--of--life-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/channel/UCFeDpvjU58SA9V0ycRXejhA) ## Introduction **sanger-tol/ensemblgenedownload** is a pipeline that downloads gene annotations from Ensembl into the Tree of Life directory structure. The pipeline is built using [Nextflow](https://www.nextflow.io), 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. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! On release, automated continuous integration tests run the pipeline on a full-sized dataset on the GitHub CI infrastructure. This ensures that the pipeline runs in a third-party environment, and has sensible resource allocation defaults set to run on real-world datasets. ## Pipeline summary ## Overview The pipeline takes a CSV file that contains assembly accession number, Ensembl species names (as they may differ from Tree of Life ones !), output directories, and geneset versions. Assembly accession numbers are optional. If missing, the pipeline assumes it can be retrieved from files named `ACCESSION` in the standard location on disk. The pipeline downloads the Fasta files of the genes (cdna, cds, and protein sequences) as well as the GFF3 file. All files are compressed with `bgzip`, and indexed with `samtools faidx` or `tabix`. Steps involved: - Download from Ensembl the GFF3 file, and the sequences of the genes in Fasta format. - Compress and index all Fasta files with `bgzip`, `samtools faidx`, and `samtools dict`. - Compress and index the GFF3 file with `bgzip` and `tabix`. ## Quick Start 1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.04.0`) 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_. 3. Download the pipeline and test it on a minimal dataset with a single command: ```bash nextflow run sanger-tol/ensemblgenedownload -profile test,YOURPROFILE --outdir ``` Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string. > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`. > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. 4. Start running your own analysis! ```console nextflow run sanger-tol/ensemblgenedownload --input $PWD/assets/samplesheet.csv --outdir -profile ``` ## Documentation The sanger-tol/ensemblgenedownload pipeline comes with documentation about the pipeline [usage](docs/usage.md) and [output](docs/output.md). ## Credits sanger-tol/ensemblgenedownload was originally written by @muffato. ## Contributions and Support If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). For further information or help, don't hesitate to get in touch on the [Slack `#pipelines` channel](https://sangertreeoflife.slack.com/channels/pipelines). Please [create an issue](https://github.com/sanger-tol/ensemblgenedownload/issues/new/choose) on GitHub if you are not on the Sanger slack channel. ## Citations If you use sanger-tol/ensemblgenedownload for your analysis, please cite it using the following doi: [10.5281/zenodo.7183206](https://doi.org/10.5281/zenodo.7183206) An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE). > **The nf-core framework for community-curated bioinformatics pipelines.** > > Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. > > _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).

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License
  MIT

## Contents

Main Workflow: sanger-tol/insdcdownload v1.0.1 - Hefty mûmakil
Size: 1705 bytes