# ![sanger-tol/insdcdownload](docs/images/sanger-tol-insdcdownload_logo.png)

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## Introduction

**sanger-tol/insdcdownload** is a pipeline that downloads assemblies from INSDC into a 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 an assembly accession number, as well as the assembly name, and downloads it. It also builds a set of common indices (such as `samtools faidx`), and extracts the repeat-masking performed by the NCBI.

Steps involved:

- Download from the NCBI the genomic sequence (Fasta) and the assembly
  stats and reports files.
- Turn the masked Fasta file into an unmasked one.
- Compress and index all Fasta files with `bgzip`, `samtools faidx`, and
  `samtools dict`.
- Generate the `.sizes` file usually required for conversion of data
  files to UCSC's "big" formats, e.g. bigBed.
- Extract the coordinates of the masked regions into a BED file.
- Compress and index the BED 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/insdcdownload -profile test,YOURPROFILE --outdir <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 <institute>` 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/insdcdownload --assembly_accession GCA_927399515.1 --assembly_name gfLaeSulp1.1 --outdir results
   ```

## Documentation

The sanger-tol/insdcdownload pipeline comes with documentation about the pipeline [usage](docs/usage.md) and [output](docs/output.md).

## Credits

sanger-tol/insdcdownload was mainly written by @muffato, with major borrowings from @priyanka-surana's [read-mapping](https://github.com/sanger-tol/readmapping) pipeline, e.g. the script to remove the repeat-masking, and the overall structure and layout of the sub-workflows.

## 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/insdcdownload/issues/new/choose) on GitHub if you are not on the Sanger slack channel.

## Citations

If you use sanger-tol/insdcdownload for your analysis, please cite it using the following doi: [10.5281/zenodo.7155119](https://doi.org/10.5281/zenodo.7155119)

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).
