From 1e767869a6213cf799259581a3da7621520fa64c Mon Sep 17 00:00:00 2001 From: drpatelh Date: Thu, 2 May 2019 22:41:56 +0100 Subject: [PATCH 1/5] Add nf-core citation --- README.md | 5 +++++ .../{{cookiecutter.name_noslash}}/README.md | 9 +++++++++ 2 files changed, 14 insertions(+) diff --git a/README.md b/README.md index 84c3f8b3e8..fcd7414cb0 100644 --- a/README.md +++ b/README.md @@ -429,3 +429,8 @@ INFO: Updating version in Singularity ``` To change the required version of Nextflow instead of the pipeline version number, use the flag `--nextflow`. + +## Citation + +If you use `nf-core tools` in your work, please cite it as follows: +Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tomasso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1). diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md index db24d0d1c4..b345988eb9 100644 --- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md +++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md @@ -28,3 +28,12 @@ The {{ cookiecutter.name }} pipeline comes with documentation about the pipeline ## Credits {{ cookiecutter.name }} was originally written by {{ cookiecutter.author }}. + + +## Citation + + + + +You can cite `nf-core` as follows: +Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tomasso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1). From ecc54fa838ae2371f4595f081ba6543f648ab0f8 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Thu, 2 May 2019 22:44:07 +0100 Subject: [PATCH 2/5] Change CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d6573a119e..0f9ec18f99 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ #### Other * Fix small typo in central readme of tools for future releases * Switched to yaml.safe_load() to fix PyYAML warning that was thrown because of a possible [exploit](https://github.com/yaml/pyyaml/wiki/PyYAML-yaml.load(input)-Deprecation) +* Add `nf-core` citation ## v1.6 From 1f88c31e36ef5829da144e7de2e635964ee44529 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 3 May 2019 09:26:32 +0100 Subject: [PATCH 3/5] Changed Paolos name by Deed Poll --- README.md | 4 ++-- .../pipeline-template/{{cookiecutter.name_noslash}}/README.md | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index fcd7414cb0..277ea8f15a 100644 --- a/README.md +++ b/README.md @@ -432,5 +432,5 @@ To change the required version of Nextflow instead of the pipeline version numbe ## Citation -If you use `nf-core tools` in your work, please cite it as follows: -Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tomasso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1). +If you use `nf-core tools` in your work, please cite the `nf-core` preprint as follows: +Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommasso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1). diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md index b345988eb9..29d5f71988 100644 --- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md +++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md @@ -36,4 +36,4 @@ The {{ cookiecutter.name }} pipeline comes with documentation about the pipeline You can cite `nf-core` as follows: -Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tomasso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1). +Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommasso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1). From c0e7a4d4cc6796f46937b1a657a0e8269ecc5592 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 3 May 2019 09:31:04 +0100 Subject: [PATCH 4/5] Add pre-print --- .../pipeline-template/{{cookiecutter.name_noslash}}/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md index 29d5f71988..8e68f5f4a1 100644 --- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md +++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md @@ -35,5 +35,5 @@ The {{ cookiecutter.name }} pipeline comes with documentation about the pipeline -You can cite `nf-core` as follows: +You can cite the `nf-core` pre-print as follows: Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommasso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1). From 13435be7fdf4994ebb82b54c1868482c76637967 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 3 May 2019 09:34:49 +0100 Subject: [PATCH 5/5] I dont speak Italian --- README.md | 2 +- .../pipeline-template/{{cookiecutter.name_noslash}}/README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 277ea8f15a..0a9e43f257 100644 --- a/README.md +++ b/README.md @@ -433,4 +433,4 @@ To change the required version of Nextflow instead of the pipeline version numbe ## Citation If you use `nf-core tools` in your work, please cite the `nf-core` preprint as follows: -Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommasso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1). +Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1). diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md index 8e68f5f4a1..cd760421b7 100644 --- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md +++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md @@ -36,4 +36,4 @@ The {{ cookiecutter.name }} pipeline comes with documentation about the pipeline You can cite the `nf-core` pre-print as follows: -Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommasso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1). +Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1).