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Add DOI and back to dev #74

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Jan 8, 2025
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2 changes: 2 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -8,10 +8,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Added

- [72](https://github.com/nf-core/references/pull/72) - Compress vcf files when they are not already compressed
- [74](https://github.com/nf-core/references/pull/74) - Add DOI

### Changed

- [73](https://github.com/nf-core/references/pull/73) - Update modules
- [74](https://github.com/nf-core/references/pull/74) - Back to dev

### Fixed

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5 changes: 2 additions & 3 deletions README.md
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Expand Up @@ -6,7 +6,7 @@
</h1>

[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/ci.yml)
[![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
[![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.14576225-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14576225)
[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)

[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.10.1-23aa62.svg)](https://www.nextflow.io/)
Expand Down Expand Up @@ -100,8 +100,7 @@ Other nice things to have:

## Citations

<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
<!-- If you use nf-core/references for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
If you use nf-core/references for your analysis, please cite it using the following doi: [10.5281/zenodo.14576225](https://doi.org/10.5281/zenodo.14576225)

<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->

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4 changes: 2 additions & 2 deletions assets/multiqc_config.yml
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/references/releases/tag/0.1" target="_blank">nf-core/references</a>
This report has been generated by the <a href="https://github.com/nf-core/references/tree/dev" target="_blank">nf-core/references</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/references/0.1/docs/output" target="_blank">documentation</a>.
<a href="https://nf-co.re/references/dev/docs/output" target="_blank">documentation</a>.
report_section_order:
"nf-core-references-methods-description":
order: -1000
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4 changes: 2 additions & 2 deletions nextflow.config
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Expand Up @@ -224,8 +224,8 @@ manifest {
description = """help community build references"""
mainScript = 'main.nf'
nextflowVersion = '!>=24.10.1'
version = '0.1'
doi = ''
version = '1.0.0dev'
doi = '10.5281/zenodo.14576225'
}

// Nextflow plugins
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4 changes: 2 additions & 2 deletions tests/hisat2.nf.test.snap
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Expand Up @@ -7,7 +7,7 @@
"hisat2": "2.2.1"
},
"Workflow": {
"nf-core/references": "v0.1"
"nf-core/references": "v1.0.0dev"
}
},
[
Expand Down Expand Up @@ -71,7 +71,7 @@
"hisat2": "2.2.1"
},
"Workflow": {
"nf-core/references": "v0.1"
"nf-core/references": "v1.0.0dev"
}
},
[
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4 changes: 2 additions & 2 deletions tests/kallisto.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
"star": "2.7.10a"
},
"Workflow": {
"nf-core/references": "v0.1"
"nf-core/references": "v1.0.0dev"
}
},
[
Expand Down Expand Up @@ -63,7 +63,7 @@
"kallisto": "0.51.1"
},
"Workflow": {
"nf-core/references": "v0.1"
"nf-core/references": "v1.0.0dev"
}
},
[
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4 changes: 2 additions & 2 deletions tests/multiple.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
"tabix": 1.2
},
"Workflow": {
"nf-core/references": "v0.1"
"nf-core/references": "v1.0.0dev"
}
},
[
Expand Down Expand Up @@ -63,7 +63,7 @@
"samtools": 1.21
},
"Workflow": {
"nf-core/references": "v0.1"
"nf-core/references": "v1.0.0dev"
}
},
[
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2 changes: 1 addition & 1 deletion tests/rnaseq.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@
"gawk": "5.1.0"
},
"Workflow": {
"nf-core/references": "v0.1"
"nf-core/references": "v1.0.0dev"
}
},
[
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4 changes: 2 additions & 2 deletions tests/rsem.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
"star": "2.7.10a"
},
"Workflow": {
"nf-core/references": "v0.1"
"nf-core/references": "v1.0.0dev"
}
},
[
Expand Down Expand Up @@ -105,7 +105,7 @@
"star": "2.7.10a"
},
"Workflow": {
"nf-core/references": "v0.1"
"nf-core/references": "v1.0.0dev"
}
},
[
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4 changes: 2 additions & 2 deletions tests/salmon.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
"salmon": "1.10.3"
},
"Workflow": {
"nf-core/references": "v0.1"
"nf-core/references": "v1.0.0dev"
}
},
[
Expand Down Expand Up @@ -87,7 +87,7 @@
"salmon": "1.10.3"
},
"Workflow": {
"nf-core/references": "v0.1"
"nf-core/references": "v1.0.0dev"
}
},
[
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6 changes: 3 additions & 3 deletions tests/samtools.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
1,
{
"Workflow": {
"nf-core/references": "v0.1"
"nf-core/references": "v1.0.0dev"
}
},
[
Expand Down Expand Up @@ -38,7 +38,7 @@
"gawk": "5.3.0"
},
"Workflow": {
"nf-core/references": "v0.1"
"nf-core/references": "v1.0.0dev"
}
},
[
Expand Down Expand Up @@ -83,7 +83,7 @@
"samtools": 1.21
},
"Workflow": {
"nf-core/references": "v0.1"
"nf-core/references": "v1.0.0dev"
}
},
[
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2 changes: 1 addition & 1 deletion tests/sarek.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@
"tabix": 1.2
},
"Workflow": {
"nf-core/references": "v0.1"
"nf-core/references": "v1.0.0dev"
}
},
[
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4 changes: 2 additions & 2 deletions tests/tabix.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
1,
{
"Workflow": {
"nf-core/references": "v0.1"
"nf-core/references": "v1.0.0dev"
}
},
[
Expand Down Expand Up @@ -41,7 +41,7 @@
"tabix": 1.2
},
"Workflow": {
"nf-core/references": "v0.1"
"nf-core/references": "v1.0.0dev"
}
},
[
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2 changes: 1 addition & 1 deletion tests/wbcel235.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@
"gawk": "5.1.0"
},
"Workflow": {
"nf-core/references": "v0.1"
"nf-core/references": "v1.0.0dev"
}
},
[
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