# ![nf-core/fetchngs](docs/images/nf-core-fetchngs_logo_light.png#gh-light-mode-only) ![nf-core/fetchngs](docs/images/nf-core-fetchngs_logo_dark.png#gh-dark-mode-only)

[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/fetchngs/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.5070524-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.5070524)

[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.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/)
[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/fetchngs)

[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23fetchngs-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/fetchngs)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)

## Introduction

**nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from both public and private databases. At present, the pipeline supports SRA / ENA / DDBJ / GEO / Synapse ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).

## Usage

> **Note**
> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
> with `-profile test` before running the workflow on actual data.

First, prepare a samplesheet with your input data that looks as follows:

`ids.csv`:

```csv
SRR9984183
SRR13191702
ERR1160846
ERR1109373
DRR028935
DRR026872
```

Each line represents a database id. Please see next section for supported ids.

Now, you can run the pipeline using:

```bash
nextflow run nf-core/fetchngs \
   -profile <docker/singularity/.../institute> \
   --input ids.csv \
   --outdir <OUTDIR>
```

> **Warning:**
> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).

For more details, please refer to the [usage documentation](https://nf-co.re/fetchngs/usage) and the [parameter documentation](https://nf-co.re/fetchngs/parameters).

## Supported ids

Via a single file of ids, provided one-per-line (see [example input file](https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv)) the pipeline performs the following steps:

### SRA / ENA / DDBJ / GEO ids

1. Resolve database ids back to appropriate experiment-level ids and to be compatible with the [ENA API](https://ena-docs.readthedocs.io/en/latest/retrieval/programmatic-access.html)
2. Fetch extensive id metadata via ENA API
3. Download FastQ files:
   - If direct download links are available from the ENA API, fetch in parallel via `curl` and perform `md5sum` check
   - Otherwise use [`sra-tools`](https://github.com/ncbi/sra-tools) to download `.sra` files and convert them to FastQ
4. Collate id metadata and paths to FastQ files in a single samplesheet

### Synapse ids

1. Resolve Synapse directory ids to their corresponding FastQ files ids via the `synapse list` command.
2. Retrieve FastQ file metadata including FastQ file names, md5sums, etags, annotations and other data provenance via the `synapse show` command.
3. Download FastQ files in parallel via `synapse get`
4. Collate paths to FastQ files in a single samplesheet

## Pipeline output

The columns in the output samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines (see [usage docs](https://nf-co.re/fetchngs/usage#samplesheet-format)), these currently include:

- [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input)
- [nf-core/atacseq](https://nf-co.re/atacseq/usage#samplesheet-input)
- Ilumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format)
- [nf-core/taxprofiler](https://nf-co.re/nf-core/taxprofiler)

To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/fetchngs/results) tab on the nf-core website pipeline page.
For more details about the output files and reports, please refer to the
[output documentation](https://nf-co.re/fetchngs/output).

## Credits

nf-core/fetchngs was originally written by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [Seqera Labs, Spain](https://seqera.io/) and Jose Espinosa-Carrasco ([@JoseEspinosa](https://github.com/JoseEspinosa)) from [The Comparative Bioinformatics Group](https://www.crg.eu/en/cedric_notredame) at [The Centre for Genomic Regulation, Spain](https://www.crg.eu/). Support for download of sequencing reads without FTP links via sra-tools was added by Moritz E. Beber ([@Midnighter](https://github.com/Midnighter)) from [Unseen Bio ApS, Denmark](https://unseenbio.com). The Synapse workflow was added by Daisy Han [@daisyhan97](https://github.com/daisyhan97) and Bruno Grande [@BrunoGrandePhD](https://github.com/BrunoGrandePhD) from [Sage Bionetworks, Seattle](https://sagebionetworks.org/).

## 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 `#fetchngs` channel](https://nfcore.slack.com/channels/fetchngs) (you can join with [this invite](https://nf-co.re/join/slack)).

## Citations

If you use nf-core/fetchngs for your analysis, please cite it using the following doi: [10.5281/zenodo.5070524](https://doi.org/10.5281/zenodo.5070524)

An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.

You can cite the `nf-core` publication as follows:

> **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).
