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Merge pull request nf-core#662 from chriswyatt1/chriswyatt1-patch-1
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README.md

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# ![nfcore/test-datasets](docs/images/test-datasets_logo.png)
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Test data to be used for automated testing with the nf-core pipelines
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## test-datasets: MELT module
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## Introduction
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This branch contains test data to be used for automated testing with the nf-core/module/melt.
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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.
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## Content of this repository
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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.
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### MELT requires transposon .zip files to direct MEI discovery.
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## Documentation
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testdata/ALU_MELT.zip: ALU transposon info (Hg38)
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nf-core/test-datasets comes with documentation in the `docs/` directory:
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testdata/HERVK_MELT.zip: HERVK transposon info (Hg38)
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01. [Add a new test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/ADD_NEW_DATA.md)
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02. [Use an existing test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/USE_EXISTING_DATA.md)
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testdata/LINE1_MELT.zip: LINE1 transposon info (Hg38)
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## Downloading test data
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testdata/SVA_MELT.zip: SVA transposon info (Hg38)
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Due the large number of large files in this repository for each pipeline, we highly recommend cloning only the branches you would use.
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```bash
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git clone <url> --single-branch --branch <pipeline/modules/branch_name>
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```
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To subsequently clone other branches[^1]
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### 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)
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```bash
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git remote set-branches --add origin [remote-branch]
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git fetch
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```
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testdata/AluY.deletion.bed : bed file for ALU Y deletion (Hg38)
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testdata/LINE1.deletion.bed : bed file for LINE1 deletion (Hg38)
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testdata/Hg38.genes.bed : bed file for genes (Hg38)
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## Support
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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).
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[^1]: From [stackoverflow](https://stackoverflow.com/a/60846265/11502856)

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