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Revert README back to correct text #662

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34 changes: 20 additions & 14 deletions README.md
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# ![nfcore/test-datasets](docs/images/test-datasets_logo.png)
Test data to be used for automated testing with the nf-core pipelines

## test-datasets: MELT module
## Introduction

This branch contains test data to be used for automated testing with the nf-core/module/melt.
nf-core is a collection of high quality Nextflow pipelines. This repository contains various files for CI and unit testing of nf-core pipelines and infrastructure.

## Content of this repository
The principle for nf-core test data is as small as possible, as large as necessary. Always ask for guidance on the [nf-core slack](https://nf-co.re/join) before adding new test data.

### MELT requires transposon .zip files to direct MEI discovery.
## Documentation

testdata/ALU_MELT.zip: ALU transposon info (Hg38)
nf-core/test-datasets comes with documentation in the `docs/` directory:

testdata/HERVK_MELT.zip: HERVK transposon info (Hg38)
01. [Add a new test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/ADD_NEW_DATA.md)
02. [Use an existing test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/USE_EXISTING_DATA.md)

testdata/LINE1_MELT.zip: LINE1 transposon info (Hg38)
## Downloading test data

testdata/SVA_MELT.zip: SVA transposon info (Hg38)
Due the large number of large files in this repository for each pipeline, we highly recommend cloning only the branches you would use.

```bash
git clone <url> --single-branch --branch <pipeline/modules/branch_name>
```

To subsequently clone other branches[^1]

### MELT requires Gene Annotation in BED format. For details and structure of this bed files, see table 2 in the [MELT documentation](https://melt.igs.umaryland.edu/manual.php)
```bash
git remote set-branches --add origin [remote-branch]
git fetch
```

testdata/AluY.deletion.bed : bed file for ALU Y deletion (Hg38)

testdata/LINE1.deletion.bed : bed file for LINE1 deletion (Hg38)

testdata/Hg38.genes.bed : bed file for genes (Hg38)
## Support

For further information or help, don't hesitate to get in touch on our [Slack organisation](https://nf-co.re/join/slack) (a tool for instant messaging).

[^1]: From [stackoverflow](https://stackoverflow.com/a/60846265/11502856)