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1 | 1 | #  |
2 | 2 | Test data to be used for automated testing with the nf-core pipelines |
3 | 3 |
|
4 | | -## test-datasets: MELT module |
| 4 | +## Introduction |
5 | 5 |
|
6 | | -This branch contains test data to be used for automated testing with the nf-core/module/melt. |
| 6 | +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. |
7 | 7 |
|
8 | | -## Content of this repository |
| 8 | +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. |
9 | 9 |
|
10 | | -### MELT requires transposon .zip files to direct MEI discovery. |
| 10 | +## Documentation |
11 | 11 |
|
12 | | - testdata/ALU_MELT.zip: ALU transposon info (Hg38) |
| 12 | +nf-core/test-datasets comes with documentation in the `docs/` directory: |
13 | 13 |
|
14 | | - testdata/HERVK_MELT.zip: HERVK transposon info (Hg38) |
| 14 | +01. [Add a new test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/ADD_NEW_DATA.md) |
| 15 | +02. [Use an existing test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/USE_EXISTING_DATA.md) |
15 | 16 |
|
16 | | - testdata/LINE1_MELT.zip: LINE1 transposon info (Hg38) |
| 17 | +## Downloading test data |
17 | 18 |
|
18 | | - testdata/SVA_MELT.zip: SVA transposon info (Hg38) |
| 19 | +Due the large number of large files in this repository for each pipeline, we highly recommend cloning only the branches you would use. |
19 | 20 |
|
| 21 | +```bash |
| 22 | +git clone <url> --single-branch --branch <pipeline/modules/branch_name> |
| 23 | +``` |
20 | 24 |
|
| 25 | +To subsequently clone other branches[^1] |
21 | 26 |
|
22 | | -### 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) |
| 27 | +```bash |
| 28 | +git remote set-branches --add origin [remote-branch] |
| 29 | +git fetch |
| 30 | +``` |
23 | 31 |
|
24 | | - testdata/AluY.deletion.bed : bed file for ALU Y deletion (Hg38) |
25 | | - |
26 | | - testdata/LINE1.deletion.bed : bed file for LINE1 deletion (Hg38) |
27 | | - |
28 | | - testdata/Hg38.genes.bed : bed file for genes (Hg38) |
| 32 | +## Support |
29 | 33 |
|
| 34 | +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). |
30 | 35 |
|
| 36 | +[^1]: From [stackoverflow](https://stackoverflow.com/a/60846265/11502856) |
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