diff --git a/README.md b/README.md index d6be26e..25a0114 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # nf-modules -Reusable modules and subworkflows for Nextflow pipelines +Reusable [modules](https://ccbr.github.io/nf-modules/docs/modules.html) and [subworkflows](https://ccbr.github.io/nf-modules/docs/subworkflows.html) for Nextflow pipelines [![test](https://github.com/CCBR/nf-modules/actions/workflows/test.yml/badge.svg)](https://github.com/CCBR/nf-modules/actions/workflows/test.yml) [![docs](https://img.shields.io/badge/docs-📖-blue)](https://ccbr.github.io/nf-modules/) @@ -34,6 +34,8 @@ nf-core subworkflows \ update [subworkflow] ``` +View listings of available [modules](https://ccbr.github.io/nf-modules/docs/modules.html) and [subworkflows](https://ccbr.github.io/nf-modules/docs/subworkflows.html) on the [documentation website](https://ccbr.github.io/nf-modules/). + ## Help & Contributing Come across a **bug**? Open an [issue](https://github.com/CCBR/nf-modules/issues) and include a minimal reproducible example. diff --git a/_quarto.yml b/_quarto.yml index 0b41178..e6ec055 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -15,24 +15,32 @@ website: search: location: navbar type: textbox + page-navigation: true + sidebar: + - id: home + title: home + contents: + - text: home + file: docs/index.qmd + - section: project info + contents: + - text: Citation + file: docs/cite.qmd + - text: Contributing + file: .github/CONTRIBUTING.md + - href: docs/contributors.qmd + - text: License + file: LICENSE.md + - text: Changelog + file: CHANGELOG.md navbar: - title: false left: - - text: home - file: docs/index.qmd + - sidebar:home - text: modules file: docs/modules.qmd - text: subworkflows file: docs/subworkflows.qmd right: - - icon: list - menu: - - text: Contributing - file: .github/CONTRIBUTING.md - - text: Changelog - file: CHANGELOG.md - - text: License - file: LICENSE.md - icon: github href: https://github.com/CCBR/nf-modules diff --git a/docs/cite.qmd b/docs/cite.qmd new file mode 100644 index 0000000..1090271 --- /dev/null +++ b/docs/cite.qmd @@ -0,0 +1,18 @@ + +Please cite this software if you use it in a publication: + +```{python} +#| echo: false +#| output: asis +!ccbr_tools cite ../CITATION.cff -f apalike | sed -E 's/^/> /g' +``` + +### Bibtex entry + +```{python} +#| echo: false +#| output: asis +print('```bibtex') +!ccbr_tools cite ../CITATION.cff -f bibtex +print('```') +``` diff --git a/docs/contributors.qmd b/docs/contributors.qmd new file mode 100644 index 0000000..74ba163 --- /dev/null +++ b/docs/contributors.qmd @@ -0,0 +1,33 @@ +--- +title: Contributors +--- + +::: {layout-ncol=5} + +```{python} +#| echo: false +#| output: asis +import requests + +def get_url_json(url): + r = requests.get(url) + data = r.json() if r.status_code == 200 else dict() + return data + + +repo = 'nf-modules' +contribs = get_url_json(f'https://api.github.com/repos/CCBR/{repo}/contributors') + +for contrib in contribs: + user_login = contrib['login'] + user_info = get_url_json(f"https://api.github.com/users/{user_login}") + user_name = user_info['name'] if user_info['name'] else user_login + avatar_url = contrib['avatar_url'] + profile_url = contrib['html_url'] + print(f"[![{user_name}]({avatar_url})]({profile_url}){{width=80px height=80px}}\n") +``` + +::: + + +View the [contributors graph on GitHub](https://github.com/CCBR/nf-modules/graphs/contributors) for more details. diff --git a/docs/requirements.txt b/docs/requirements.txt index 4f313b7..fb27a80 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,2 +1,3 @@ ruamel.yaml ruamel.yaml.string +git+https://github.com/CCBR/Tools.git