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c11d9b5
add logo + update README
maxulysse Aug 9, 2018
38f5fa7
Merge pull request #6 from MaxUlysse/master
maxulysse Aug 9, 2018
6c11acb
Added atacseq specific info
drpatelh Oct 10, 2018
519d480
Remove docs
drpatelh Oct 10, 2018
c87db2c
initial commit
drpatelh Oct 10, 2018
1ccd163
Merge pull request #13 from drpatelh/atacseq
apeltzer Oct 19, 2018
996dcf7
chipseq test data
ewels Jun 12, 2018
e59a30a
Add bed and gtf files for chipseq test
chuan-wang Aug 22, 2018
2aa0d7a
Updated all files for iGenomes R64-1-1 Ensembl release
drpatelh Oct 26, 2018
e201e43
Update design.csv
drpatelh Feb 15, 2019
cd07ec0
Removed nf-core chipseq test data
drpatelh Feb 18, 2019
d8d630f
Add newly built test dataset
drpatelh Feb 18, 2019
73a1fa0
Changed design
drpatelh Feb 18, 2019
78fdcbc
Removed genes.bed
drpatelh Feb 18, 2019
277833a
Change links to pubmed and GEO
drpatelh Feb 18, 2019
691b085
Merge pull request #29 from drpatelh/atacseq
ewels Feb 18, 2019
72da6b0
fix typos, closes #14
maxulysse Apr 30, 2019
470a72e
Merge pull request #47 from MaxUlysse/master
drpatelh Apr 30, 2019
4e19b5d
change gitter for slack
maxulysse Apr 30, 2019
382ae2c
Merge remote-tracking branch 'upstream/master'
maxulysse Apr 30, 2019
de901ee
Merge pull request #49 from MaxUlysse/master
apeltzer Apr 30, 2019
298a362
Fix slack invite URL
ewels Jul 30, 2019
e5cdd0d
Merge pull request #63 from ewels/master
apeltzer Jul 30, 2019
438bb95
add social preview image
maxulysse Feb 11, 2020
8e3b6ac
Merge pull request #116 from MaxUlysse/master
ewels Mar 6, 2020
46c8a2b
Add full design
drpatelh Mar 26, 2020
2b2b800
Update README
drpatelh Mar 26, 2020
ea8c8ec
Update README
drpatelh Mar 26, 2020
277d72f
Add spaces
drpatelh Mar 26, 2020
5095f43
Add more spaces
drpatelh Mar 26, 2020
6faea89
Fix headers
drpatelh Mar 26, 2020
d4f0727
Merge pull request #136 from drpatelh/atacseq
drpatelh Mar 26, 2020
74d9e7a
Update design_full.csv
drpatelh Jul 1, 2020
a66b00c
Update README.md
drpatelh Jul 1, 2020
a21479a
Update README.md
reganhayward Sep 7, 2020
b2a4326
Delete ADD_NEW_DATA.md
reganhayward Sep 7, 2020
59de154
Delete USE_EXISTING_DATA.md
reganhayward Sep 7, 2020
9abde3c
Delete test-datasets_logo.svg
reganhayward Sep 7, 2020
cc46f40
Delete test-datasets_logo.png
reganhayward Sep 7, 2020
418b0a1
Delete nf-core-test-datasets_social_preview.png
reganhayward Sep 7, 2020
ab62971
Delete nf-core-test-datasets_social_preview.svg
reganhayward Sep 7, 2020
8a3bb93
Add files via upload
reganhayward Sep 7, 2020
486fe00
Rename SL1344_sub.gff3 to references/SL1344_sub.gff3
reganhayward Sep 7, 2020
d8614db
Add files via upload
reganhayward Sep 7, 2020
9df5709
Add files via upload
reganhayward Sep 7, 2020
f0e35cb
Create sample_01_1.fq.gz
reganhayward Sep 7, 2020
1037394
Add files via upload
reganhayward Sep 7, 2020
beaa3cb
Delete sample_01_1.fq.gz
reganhayward Sep 7, 2020
81f5391
Add files via upload
reganhayward Sep 7, 2020
9c7be4e
Merge pull request #179 from reganhayward/dualrnaseq
reganhayward Sep 28, 2020
ed414e1
Revert "dualrnaseq"
drpatelh Sep 29, 2020
5e348ce
Merge pull request #186 from nf-core/revert-179-dualrnaseq
drpatelh Sep 29, 2020
0c58a9f
Update design_full.csv
drpatelh Nov 5, 2020
9a3c48e
feat: remove social preview image to use GitHub OpenGraph
maxulysse Apr 26, 2021
6869b13
Merge pull request #245 from maxulysse/master
ewels Apr 26, 2021
ef015f8
add test dataset for hicar
jianhong Aug 9, 2021
c443047
Merge pull request #312 from jianhong/hicar
jianhong Aug 9, 2021
ec1d7d9
Revert "add test dataset for hicar"
jianhong Aug 9, 2021
ecfd4af
Merge pull request #313 from nf-core/revert-312-hicar
jianhong Aug 9, 2021
3fc6eb7
📦 NEW: Add test data for isoseq modules tests
sguizard Aug 13, 2021
e79a8ea
📦 NEW: Add primers sequences
sguizard Aug 13, 2021
e08ac99
📦 NEW: add raw reads
sguizard Aug 13, 2021
6c07070
👌 IMPROVE: Remove files not used in tests
sguizard Aug 13, 2021
46447c4
docs: Update from travis-ci to github workflows
edmundmiller Oct 15, 2021
a8c0778
docs: Add note about git clone --depth 1
edmundmiller Oct 15, 2021
4568517
docs: Recommend --single-branch instead of --depth 1
edmundmiller Oct 15, 2021
0201302
Update documentation on how 'big' and how to single-branch clone
jfy133 Nov 26, 2021
7c3d636
Merge pull request #361 from Emiller88/master
heuermh Dec 16, 2021
f876097
Added test-data for nf-core/circdna; Added readme
DSchreyer Mar 7, 2022
c1e3814
Added samplesheet
DSchreyer Mar 7, 2022
1588454
New reference genoem
DSchreyer Mar 7, 2022
59ad419
New test-data; new reference genome; new samplesheet
DSchreyer Mar 7, 2022
6d3409d
Removed test-data
DSchreyer Mar 9, 2022
72fb9a3
Update
DSchreyer Mar 9, 2022
c734363
Refined samplesheet with download fastqs
DSchreyer Mar 17, 2022
dece64a
Merge pull request #470 from DSchreyer/circdna
Mar 17, 2022
3cd7a46
Revert "Circdna"
Mar 17, 2022
55ea7d4
Merge pull request #471 from nf-core/revert-470-circdna
Mar 17, 2022
867303b
remove useless files
sguizard Apr 7, 2022
5c8834d
add data
sguizard Apr 7, 2022
90d5c76
Reorganize data
sguizard Apr 7, 2022
679ea85
👌 IMPROVE: Add samplesheet.csv
sguizard Apr 15, 2022
fc20d87
Add: samplesheets and readme
praveenraj2018 May 5, 2022
74356e8
Edit: readme
praveenraj2018 May 5, 2022
46a2860
Merge pull request #527 from nf-core/rnavar
maxulysse May 5, 2022
49a701f
Revert "Samplesheets for rnavar pipeline"
maxulysse May 5, 2022
fe0b744
Merge pull request #528 from nf-core/revert-527-rnavar
maxulysse May 5, 2022
4e2077e
👌 IMPROVE: Add samplesheet_full.csv
sguizard May 12, 2022
041203b
🐛 FIX: Correct half 🐷, half 🐔, half 🧸 dataset
sguizard May 17, 2022
96bc5dc
Terminate 🐔
sguizard May 18, 2022
7fdf438
📦 ADD: full test primers
sguizard May 18, 2022
fabb1e8
Move pbi to nf-core bucket
sguizard Jun 15, 2022
ac71afc
Merge pull request #559 from sguizard/isoseq
sguizard Jun 15, 2022
a39d491
Revert Isoseq
sguizard Jun 20, 2022
df25105
Add `CITATION.cff` for the nf-core publication
ErikDanielsson Jul 12, 2022
13c222f
Merge pull request #569 from nf-core/add-citation-cff
apeltzer Jul 12, 2022
62aec2a
Update CITATION.cff
maxulysse Oct 11, 2022
67e650c
Add file via Upload to test the melt module
scorreard Oct 11, 2022
7bcc19b
Create remove
scorreard Oct 11, 2022
25c5740
Added file via upload to test melt module
scorreard Oct 11, 2022
6ee0c34
Delete ALU_MELT.zip
scorreard Oct 11, 2022
f6ffb9b
Delete AluY.deletion.bed
scorreard Oct 11, 2022
b4bd76b
Delete HERVK_MELT.zip
scorreard Oct 11, 2022
7f3c741
Delete Hg38.genes.bed
scorreard Oct 11, 2022
ea6cf47
Delete LINE1.deletion.bed
scorreard Oct 11, 2022
0124250
Delete SVA_MELT.zip
scorreard Oct 11, 2022
68d661d
Delete LINE1_MELT.zip
scorreard Oct 11, 2022
ca427ca
Delete remove
scorreard Oct 12, 2022
c420b8e
Update README.md
scorreard Oct 12, 2022
0c1d5f8
Update README.md
scorreard Oct 12, 2022
59589cc
Update README.md
scorreard Oct 12, 2022
03fa4a1
Update README.md
scorreard Oct 12, 2022
eb6802c
Merge pull request #653 from scorreard/melt
scorreard Oct 12, 2022
495584e
Revert README back to correct text
chriswyatt1 Oct 15, 2022
682bf9d
Merge pull request #662 from chriswyatt1/chriswyatt1-patch-1
apeltzer Oct 17, 2022
4e3f6a2
Delete testdata directory
scorreard Nov 16, 2022
9f9c802
Update README.md
jfy133 Nov 21, 2022
bfb959f
Merge pull request #697 from jfy133/master
jfy133 Nov 21, 2022
6b0fbde
Update README.md
jfy133 Nov 24, 2022
41d1805
Update ADD_NEW_DATA.md
jfy133 Nov 24, 2022
3b6777b
Merge pull request #700 from nf-core/readme-update
jfy133 Nov 25, 2022
5815d2c
Merge pull request #650 from nf-core/maxulysse-patch-1
maxulysse Jun 3, 2023
74e0093
Added test dataset for rastair in methylseq
eduard-watchmaker Sep 11, 2025
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56 changes: 56 additions & 0 deletions CITATION.cff
Original file line number Diff line number Diff line change
@@ -0,0 +1,56 @@
cff-version: 1.2.0
message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication"
authors:
- family-names: Ewels
given-names: Philip
- family-names: Peltzer
given-names: Alexander
- family-names: Fillinger
given-names: Sven
- family-names: Patel
given-names: Harshil
- family-names: Alneberg
given-names: Johannes
- family-names: Wilm
given-names: Andreas
- family-names: Garcia
given-names: Maxime Ulysse
- family-names: Di Tommaso
given-names: Paolo
- family-names: Nahnsen
given-names: Sven
title: "The nf-core framework for community-curated bioinformatics pipelines."
version: 2.4.1
doi: 10.1038/s41587-020-0439-x
date-released: 2022-05-16
url: https://github.com/nf-core/tools
prefered-citation:
type: article
authors:
- family-names: Ewels
given-names: Philip
- family-names: Peltzer
given-names: Alexander
- family-names: Fillinger
given-names: Sven
- family-names: Patel
given-names: Harshil
- family-names: Alneberg
given-names: Johannes
- family-names: Wilm
given-names: Andreas
- family-names: Garcia
given-names: Maxime Ulysse
- family-names: Di Tommaso
given-names: Paolo
- family-names: Nahnsen
given-names: Sven
doi: 10.1038/s41587-020-0439-x
journal: nature biotechnology
start: 276
end: 278
title: "The nf-core framework for community-curated bioinformatics pipelines."
issue: 3
volume: 38
year: 2020
url: https://dx.doi.org/10.1038/s41587-020-0439-x
38 changes: 37 additions & 1 deletion README.md
Original file line number Diff line number Diff line change
@@ -1,2 +1,38 @@
# test-datasets
# ![nfcore/test-datasets](docs/images/test-datasets_logo.png)
Test data to be used for automated testing with the nf-core pipelines

> ⚠️ **Do not merge your test data to `master`! Each pipeline has a dedicated branch (and a special one for modules)**

## Introduction

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.

The principle for nf-core test data is as small as possible, as large as necessary. Please see the [guidelines](https://nf-co.re/docs/contributing/test_data_guidelines) for more detailed information. Always ask for guidance on the [nf-core slack](https://nf-co.re/join) before adding new test data.

## Documentation

nf-core/test-datasets comes with documentation in the `docs/` directory:

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)

## Downloading test data

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]

```bash
git remote set-branches --add origin [remote-branch]
git fetch
```

## 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)
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