From 848513acd8c4b8b0eb757a99b405c6af26e63260 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 31 Oct 2024 08:39:43 +1030 Subject: [PATCH 01/31] Add tiles to index.md --- index.md | 11 +++++++++++ project/index.md | 2 -- 2 files changed, 11 insertions(+), 2 deletions(-) diff --git a/index.md b/index.md index 5c9cf94..e7e154f 100644 --- a/index.md +++ b/index.md @@ -11,10 +11,13 @@ sidebar: true This website describes the open source **project** for developing and running [WorkflowHub](https://workflowhub.eu/). +{% include section-navigation-tiles-simple.html col = "2" custom="index, news" sort=false %} + For more details, see [About WorkflowHub](/project), [FAIR Computational Workflows](https://workflows.community/groups/fair/), [Outreach and Publications](/project/outreach). For any kind of questions or suggestions on using WorkflowHub, feel free to join our [community](/project/community)! + ## Documentation * [Documentation & Quick Start guide](docs/) (See also _Detailed Documentation_) @@ -24,6 +27,7 @@ For any kind of questions or suggestions on using WorkflowHub, feel free to join - [Make your workflows findable and citable](https://www.youtube.com/watch?v=2kGKxaPuQN8) ([slides](https://doi.org/10.5281/zenodo.7787488)) - [WorkflowHub ask-me-anything](https://workflowhub.eu/presentations/19?version=1) tutorial session + ## Project resources * **Production instance**: @@ -47,6 +51,7 @@ For any kind of questions or suggestions on using WorkflowHub, feel free to join * [Poster: The WorkflowHub, a registry for Life Science Workflows](https://workflowhub.eu/presentations/1). Ambarish Kumar, ISMB, 2020-07-13 * [WorkflowHub Introduction slides](https://drive.google.com/open?id=1hfBAjjRnL9jGoxHEvq66Wo-wuKqouR3C). Carole Goble, 2020-03-25 + ## Community Regular meeting: **WorkflowHub Club** - all welcome! @@ -58,14 +63,17 @@ Anyone is welcome to join the bi-weekly [WorkflowHub Club](/project/community) c See the list of club members on the [acknowledgement](/project/acknowledgements) page. + ## Code of conduct This project has a [Code of Conduct](https://github.com/workflowhub-eu/about/blob/master/CODE_OF_CONDUCT.md) to ensure interactions are friendly, respectful and inclusive. You can contact if you have any concerns or questions. + ## Citation {% include citation.md %} + ## Acknowledgements We are grateful for contributions from [**EOSC-Life**](https://www.eosc-life.eu/), [ELIXIR Europe](https://elixir-europe.org/), [**EuroScienceGateway**](http://eurosciencegateway.eu/) and others (see complete [list of funders](/project/acknowledgements#funding)). @@ -73,3 +81,6 @@ We are grateful for contributions from [**EOSC-Life**](https://www.eosc-life.eu +## Retention and End-of-Life policy + +WorkflowHub's sustainability plan is to ensure the availability of its contributions and metadata up to and beyond 2027. If and when the WorkflowHub reaches its end of service after that, the published contributions and metadata will be archived as RO-Crates and made available through a public repository, such as Zenodo, Figshare or another appropriate resource at that time. [DOI registrations](/docs/citable/) will in this case be updated to link to the archived deposits. diff --git a/project/index.md b/project/index.md index 88ea7e1..8dc3485 100644 --- a/project/index.md +++ b/project/index.md @@ -46,6 +46,4 @@ Aims of the project include: * Workflow snapshot preservation, publishing, citation and monitoring, credit claiming and workflows part of the scholarly communication landscape partnering with platforms like [DataCite](https://datacite.org/) and EOSC’s [OpenAIRE](https://www.openaire.eu/) and their Research Community Dashboards linking publications with workflows, associated datasets, software, etc. * The workflow registry is planned to be based on the [SEEK platform](https://seek4science.org/) using [Common Workflow Language](https://www.commonwl.org/) and [Research Objects](http://www.researchobject.org/) to glue in federated workflow and tool descriptions across the research infrastructures. -## Retention and End-of-Life policy -WorkflowHub's sustainability plan is to ensure the availability of its contributions and metadata up to and beyond 2027. If and when the WorkflowHub reaches its end of service after that, the published contributions and metadata will be archived as RO-Crates and made available through a public repository, such as Zenodo, Figshare or another appropriate resource at that time. [DOI registrations](/docs/citable/) will in this case be updated to link to the archived deposits. From 401369d81cec12109b956b8e48de6d16b094e6a2 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 31 Oct 2024 10:36:45 +1030 Subject: [PATCH 02/31] Add tiles to index.md --- docs/index.md | 1 + index.md | 2 +- project/news.md | 1 + project/outreach.md | 1 + 4 files changed, 4 insertions(+), 1 deletion(-) diff --git a/docs/index.md b/docs/index.md index f3d57f0..538664f 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,6 +1,7 @@ --- title: Quick start guide toc: false +page_id: docs redirect_from: - /docs/before-you-start/ - /docs/onboarding/ diff --git a/index.md b/index.md index e7e154f..a85d6ca 100644 --- a/index.md +++ b/index.md @@ -11,7 +11,7 @@ sidebar: true This website describes the open source **project** for developing and running [WorkflowHub](https://workflowhub.eu/). -{% include section-navigation-tiles-simple.html col = "2" custom="index, news" sort=false %} +{% include section-navigation-tiles-simple.html col = "2" custom="news, outreach, docs" sort=false %} For more details, see [About WorkflowHub](/project), [FAIR Computational Workflows](https://workflows.community/groups/fair/), [Outreach and Publications](/project/outreach). diff --git a/project/news.md b/project/news.md index ccc6de4..f9644e5 100644 --- a/project/news.md +++ b/project/news.md @@ -1,5 +1,6 @@ --- title: News +page_id: news --- {% include news.html truncate=true %} diff --git a/project/outreach.md b/project/outreach.md index 4338b1a..58054ff 100644 --- a/project/outreach.md +++ b/project/outreach.md @@ -1,5 +1,6 @@ --- title: Outreach and Publications +page_id: outreach --- From ab488927e9be8f11ed72e674c181b905274654ea Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 31 Oct 2024 10:39:37 +1030 Subject: [PATCH 03/31] Add tiles to index.md --- index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.md b/index.md index a85d6ca..d2e47a7 100644 --- a/index.md +++ b/index.md @@ -11,7 +11,7 @@ sidebar: true This website describes the open source **project** for developing and running [WorkflowHub](https://workflowhub.eu/). -{% include section-navigation-tiles-simple.html col = "2" custom="news, outreach, docs" sort=false %} +{% include section-navigation-tiles.html col = "2" custom="news, outreach, docs" sort=false %} For more details, see [About WorkflowHub](/project), [FAIR Computational Workflows](https://workflows.community/groups/fair/), [Outreach and Publications](/project/outreach). From 11727880c959b72bdf71baa34d29085a4cb0e918 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 31 Oct 2024 10:44:54 +1030 Subject: [PATCH 04/31] Update docs index.md --- docs/index.md | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/docs/index.md b/docs/index.md index 538664f..9f26c4f 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,5 +1,5 @@ --- -title: Quick start guide +title: Documentation toc: false page_id: docs redirect_from: @@ -9,16 +9,18 @@ redirect_from: --- +## Quick start guide + **WorkflowHub will help make your workflows findable and citable, and this guide will help you get started with that process.** {% include callout.html type="tip" content="if you want to test WorkflowHub and its features, there is a [development instance available here](https://dev.workflowhub.eu/)." %} -## 1. Register yourself on WorkflowHub +### 1. Register yourself on WorkflowHub Register yourself on the [sign up page](https://workflowhub.eu/signup) of WorkflowHub if you do not have an account. You can also log in using your [LS Login](https://lifescience-ri.eu/ls-login/) or [GitHub](https://github.com/) credentials. -## 2. Decide which `Space` you would like to create a `Team` in +### 2. Decide which `Space` you would like to create a `Team` in **Figure 1** below highlights the basic structure of WorkflowHub, and examples of the three types of `Spaces` where you could create a `Team`. Learn more about `Teams` and `Spaces` [here](/docs/space-team-organisation). @@ -37,7 +39,7 @@ You can request to create a `Team` in any or all of the following `Spaces`: {% include callout.html type="note" content="you can create multiple teams in multiple spaces, depending on your requirements." %} -## 3. Create a team or join an existing team +### 3. Create a team or join an existing team Go to the [create](https://workflowhub.eu/projects/guided_create) and [join](https://workflowhub.eu/projects/guided_join) a team page from WorkflowHub to do so. @@ -57,7 +59,7 @@ More information on how to join a team can be found on the [how to create and jo {% include image.html file="team.svg" caption="Fig 2. Screenshot of required minimum information (numbered) that needs to be entered into the *Create a New Team* wizard on WorkflowHub." alt="minimum information" %} -## 4. Register workflow(s) +### 4. Register workflow(s) Workflows can be registered using the [WorkflowHub wizard](https://workflowhub.eu/workflows/new) From 72eb58b37f54458715944a664632e1fa3a095e30 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 31 Oct 2024 10:46:56 +1030 Subject: [PATCH 05/31] Combine about and project index.md content --- index.md | 45 +++++++++++++++++++++++++++++++++++++++++++++ project/index.md | 43 ------------------------------------------- 2 files changed, 45 insertions(+), 43 deletions(-) diff --git a/index.md b/index.md index d2e47a7..73c6a30 100644 --- a/index.md +++ b/index.md @@ -84,3 +84,48 @@ We are grateful for contributions from [**EOSC-Life**](https://www.eosc-life.eu ## Retention and End-of-Life policy WorkflowHub's sustainability plan is to ensure the availability of its contributions and metadata up to and beyond 2027. If and when the WorkflowHub reaches its end of service after that, the published contributions and metadata will be archived as RO-Crates and made available through a public repository, such as Zenodo, Figshare or another appropriate resource at that time. [DOI registrations](/docs/citable/) will in this case be updated to link to the archived deposits. + + +* [WorkflowHub](https://workflowhub.eu) is a domain-agnostic workflow registry designed around [FAIR principles](https://workflows.community/groups/fair/). +* WorkflowHub allows workflows to be FAIR, citable, have managed *metadata* profiles, and be openly available for review and analytics. +* Workflows are packaged, registered, downloaded and exchanged as [workflow-centric Research Objects](/Workflow-RO-Crate/) using the [RO-Crate](https://w3id.org/ro/crate) specification, with test and example data, managed metadata profiles, citations and more. +* A [schema.org](https://schema.org/) based Bioschemas profile describes the metadata about a workflow and use of the [Common Workflow Language](https://www.commonwl.org/) is encouraged, providing a canonical description of the workflow itself. +* Popular workflow management systems such as [Galaxy](https://galaxyproject.org/), [Nextflow](https://nextflow.io/), and [Snakemake](https://snakemake.readthedocs.io/) are working with the Hub to seamlessly and automatically support object packaging, registration and exchange. +* WorkflowHub is *workflow management system agnostic*: workflows may remain in their native repositories in their native forms. +* WorkflowHub provides features such as community spaces, collections, versioning and snapshots, and contributor credit. +* In addition to its own [APIs](https://workflowhub.eu/api), WorkflowHub supports community registry standards and services such as [GA4GH TRS](https://about.workflowhub.eu/TRS/) and [ELIXIR-AAI](https://elixir-europe.org/services/compute/aai) authentication, and current work integrates with the [LifeMonitor workflow testing](https://lifemonitor.eu/) service. +* WorkflowHub is mainly sponsored by the European RI Cluster [EOSC-Life](https://www.eosc-life.eu/), the European Research Infrastructure [ELIXIR](https://elixir-europe.org/) and [EuroScienceGateway](http://eurosciencegateway.eu/) (see [full list of acknowledgements](/project/acknowledgements/#funding)). +* The [WorkflowHub Club](/project/community/) open community works together to continuously co-develop the Hub. +* First beta-released in Sept 2020 and production-released in September 2022, the Hub now holds over [300 workflows](https://workflowhub.eu/workflows), including 49 curated [COVID-19 workflows](https://covid19.workflowhub.eu/). It is a listed resource of the European [COVID19 Data Portal](https://www.covid19dataportal.org/) and as a [EOSC Data Source](https://marketplace.eosc-portal.eu/datasources/eosc.elixir-uk.5126ffcc8e23f65bbbe219d36128f2c8). + +## Contact Us + +The production instance is hosted by [eScience Lab](https://esciencelab.org.uk/) at [The University of Manchester](https://www.manchester.ac.uk/) led by professor [Carole Goble](https://research.manchester.ac.uk/en/persons/carole.goble). + +* [Provide feedback or ask question](https://workflowhub.eu/home/feedback) +* Contribute to [WorkflowHub club](https://about.workflowhub.eu/project/community/) (Regular telcons, Slack chat, public mailing list) +* [Report an issue](https://workflowhub.eu/home/report_issue) (public GitHub), or: + - Contact `workflowhub.eu` system administrators: + - Report [Code of Conduct](https://github.com/workflowhub-eu/about/blob/master/CODE_OF_CONDUCT.md) concerns: +* Academic collaborations: + + +## WfCommons and WorkflowHub + +Note that the US-based [WfCommons](https://wfcommons.org/), a Python-based framework for enabling scientific workflow research and development, was previously [called "WorkflowHub"](https://doi.org/10.1109/WORKS51914.2020.00012). While that framework is not related to our registry workflowhub.eu, this name collision could cause some confusion, so in common agreement with Rafael Ferreira da Silva, their former domain name `workflowhub.org` +now kindly redirect to our workflow registry , their framework was renamed to "WfCommons" and moved to and their Python package `workflowhub` was renamed [`wfcommons`](https://pypi.org/project/wfcommons/). + + + +## Development + +Created as part of the [EOSC-Life](https://www.eosc-life.eu) WP2 [Tools Collaboratory](https://github.com/eosc-life/tools-collaboratory-roadmap), WorkflowHub is in production but still under active development. + +See a complete list of contributors on the [acknowledgement](/project/acknowledgements) page. + +Aims of the project include: + +* Evolvement of [myExperiment](https://myexperiment.org/) that is workflow system agnostic, supports a repository of workflows in native and standardised form (e.g. [CWL](https://www.commonwl.org/) and the virtual aggregation of established tool, workflow and registries to support discovery over a fragmented ecosystem. The federated registry would support a **common API** to simplify access for tool developers. +* Standardised workflow identifiers and metadata descriptions needed for workflow discovery, reuse, preservation, interoperability and monitoring and metadata harvesting using standard protocols. Workflows are usually multi-component (requiring links to test data, example runs, explanatory documentation, etc) and used in collections for scientific use cases. We plan to use the Research Object specification for packaging workflows, which has already been combined with [CWL](https://www.commonwl.org/) and is part of the [BioComputeObject](http://biocomputeobject.org/) specification. +* Workflow snapshot preservation, publishing, citation and monitoring, credit claiming and workflows part of the scholarly communication landscape partnering with platforms like [DataCite](https://datacite.org/) and EOSC’s [OpenAIRE](https://www.openaire.eu/) and their Research Community Dashboards linking publications with workflows, associated datasets, software, etc. +* The workflow registry is planned to be based on the [SEEK platform](https://seek4science.org/) using [Common Workflow Language](https://www.commonwl.org/) and [Research Objects](http://www.researchobject.org/) to glue in federated workflow and tool descriptions across the research infrastructures. diff --git a/project/index.md b/project/index.md index 8dc3485..213728e 100644 --- a/project/index.md +++ b/project/index.md @@ -2,48 +2,5 @@ title: About WorkflowHub --- -* [WorkflowHub](https://workflowhub.eu) is a domain-agnostic workflow registry designed around [FAIR principles](https://workflows.community/groups/fair/). -* WorkflowHub allows workflows to be FAIR, citable, have managed *metadata* profiles, and be openly available for review and analytics. -* Workflows are packaged, registered, downloaded and exchanged as [workflow-centric Research Objects](/Workflow-RO-Crate/) using the [RO-Crate](https://w3id.org/ro/crate) specification, with test and example data, managed metadata profiles, citations and more. -* A [schema.org](https://schema.org/) based Bioschemas profile describes the metadata about a workflow and use of the [Common Workflow Language](https://www.commonwl.org/) is encouraged, providing a canonical description of the workflow itself. -* Popular workflow management systems such as [Galaxy](https://galaxyproject.org/), [Nextflow](https://nextflow.io/), and [Snakemake](https://snakemake.readthedocs.io/) are working with the Hub to seamlessly and automatically support object packaging, registration and exchange. -* WorkflowHub is *workflow management system agnostic*: workflows may remain in their native repositories in their native forms. -* WorkflowHub provides features such as community spaces, collections, versioning and snapshots, and contributor credit. -* In addition to its own [APIs](https://workflowhub.eu/api), WorkflowHub supports community registry standards and services such as [GA4GH TRS](https://about.workflowhub.eu/TRS/) and [ELIXIR-AAI](https://elixir-europe.org/services/compute/aai) authentication, and current work integrates with the [LifeMonitor workflow testing](https://lifemonitor.eu/) service. -* WorkflowHub is mainly sponsored by the European RI Cluster [EOSC-Life](https://www.eosc-life.eu/), the European Research Infrastructure [ELIXIR](https://elixir-europe.org/) and [EuroScienceGateway](http://eurosciencegateway.eu/) (see [full list of acknowledgements](/project/acknowledgements/#funding)). -* The [WorkflowHub Club](/project/community/) open community works together to continuously co-develop the Hub. -* First beta-released in Sept 2020 and production-released in September 2022, the Hub now holds over [300 workflows](https://workflowhub.eu/workflows), including 49 curated [COVID-19 workflows](https://covid19.workflowhub.eu/). It is a listed resource of the European [COVID19 Data Portal](https://www.covid19dataportal.org/) and as a [EOSC Data Source](https://marketplace.eosc-portal.eu/datasources/eosc.elixir-uk.5126ffcc8e23f65bbbe219d36128f2c8). - -## Contact Us - -The production instance is hosted by [eScience Lab](https://esciencelab.org.uk/) at [The University of Manchester](https://www.manchester.ac.uk/) led by professor [Carole Goble](https://research.manchester.ac.uk/en/persons/carole.goble). - -* [Provide feedback or ask question](https://workflowhub.eu/home/feedback) -* Contribute to [WorkflowHub club](https://about.workflowhub.eu/project/community/) (Regular telcons, Slack chat, public mailing list) -* [Report an issue](https://workflowhub.eu/home/report_issue) (public GitHub), or: - - Contact `workflowhub.eu` system administrators: - - Report [Code of Conduct](https://github.com/workflowhub-eu/about/blob/master/CODE_OF_CONDUCT.md) concerns: -* Academic collaborations: - - -## WfCommons and WorkflowHub - -Note that the US-based [WfCommons](https://wfcommons.org/), a Python-based framework for enabling scientific workflow research and development, was previously [called "WorkflowHub"](https://doi.org/10.1109/WORKS51914.2020.00012). While that framework is not related to our registry workflowhub.eu, this name collision could cause some confusion, so in common agreement with Rafael Ferreira da Silva, their former domain name `workflowhub.org` -now kindly redirect to our workflow registry , their framework was renamed to "WfCommons" and moved to and their Python package `workflowhub` was renamed [`wfcommons`](https://pypi.org/project/wfcommons/). - - - -## Development - -Created as part of the [EOSC-Life](https://www.eosc-life.eu) WP2 [Tools Collaboratory](https://github.com/eosc-life/tools-collaboratory-roadmap), WorkflowHub is in production but still under active development. - -See a complete list of contributors on the [acknowledgement](/project/acknowledgements) page. - -Aims of the project include: - -* Evolvement of [myExperiment](https://myexperiment.org/) that is workflow system agnostic, supports a repository of workflows in native and standardised form (e.g. [CWL](https://www.commonwl.org/) and the virtual aggregation of established tool, workflow and registries to support discovery over a fragmented ecosystem. The federated registry would support a **common API** to simplify access for tool developers. -* Standardised workflow identifiers and metadata descriptions needed for workflow discovery, reuse, preservation, interoperability and monitoring and metadata harvesting using standard protocols. Workflows are usually multi-component (requiring links to test data, example runs, explanatory documentation, etc) and used in collections for scientific use cases. We plan to use the Research Object specification for packaging workflows, which has already been combined with [CWL](https://www.commonwl.org/) and is part of the [BioComputeObject](http://biocomputeobject.org/) specification. -* Workflow snapshot preservation, publishing, citation and monitoring, credit claiming and workflows part of the scholarly communication landscape partnering with platforms like [DataCite](https://datacite.org/) and EOSC’s [OpenAIRE](https://www.openaire.eu/) and their Research Community Dashboards linking publications with workflows, associated datasets, software, etc. -* The workflow registry is planned to be based on the [SEEK platform](https://seek4science.org/) using [Common Workflow Language](https://www.commonwl.org/) and [Research Objects](http://www.researchobject.org/) to glue in federated workflow and tool descriptions across the research infrastructures. From 8811a5d7951fb0e0b074044256950f7f83d66d7e Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 31 Oct 2024 10:56:29 +1030 Subject: [PATCH 06/31] Update index.md and fix links --- index.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/index.md b/index.md index 73c6a30..a74e9ab 100644 --- a/index.md +++ b/index.md @@ -7,13 +7,15 @@ hide_sidebar: true sidebar: true --- -[WorkflowHub](https://workflowhub.eu/) is a FAIR **workflow registry** sponsored by the European RI Cluster EOSC-Life, the European Research Infrastructure ELIXIR and [multiple EU-wide projects](/project/acknowledgements/#funding). It is workflow management system agnostic: workflows may remain in their native repositories in their native forms. +[WorkflowHub](https://workflowhub.eu/) is a FAIR registry for describing, sharing and publishing scientific computational workflows. The registry is sponsored by the European RI Cluster EOSC-Life, the European Research Infrastructure ELIXIR, and [multiple EU-wide projects](/project/acknowledgements/#funding). + +It is workflow management system agnostic: workflows may remain in their native repositories in their native forms. This website describes the open source **project** for developing and running [WorkflowHub](https://workflowhub.eu/). {% include section-navigation-tiles.html col = "2" custom="news, outreach, docs" sort=false %} -For more details, see [About WorkflowHub](/project), [FAIR Computational Workflows](https://workflows.community/groups/fair/), [Outreach and Publications](/project/outreach). +For more details, see [About WorkflowHub](project), [FAIR Computational Workflows](https://workflows.community/groups/fair/), [Outreach and Publications](project/outreach). For any kind of questions or suggestions on using WorkflowHub, feel free to join our [community](/project/community)! From fa04704ce17592c6520566cd48570770969733e1 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 31 Oct 2024 11:02:32 +1030 Subject: [PATCH 07/31] New structure for index.md --- index.md | 50 +++++++++++++++++++++++++++----------------------- 1 file changed, 27 insertions(+), 23 deletions(-) diff --git a/index.md b/index.md index a74e9ab..d2e72f1 100644 --- a/index.md +++ b/index.md @@ -54,7 +54,14 @@ For any kind of questions or suggestions on using WorkflowHub, feel free to join * [WorkflowHub Introduction slides](https://drive.google.com/open?id=1hfBAjjRnL9jGoxHEvq66Wo-wuKqouR3C). Carole Goble, 2020-03-25 -## Community +## Citation + +{% include citation.md %} + + +## Get involved + +### Community Regular meeting: **WorkflowHub Club** - all welcome! @@ -65,15 +72,32 @@ Anyone is welcome to join the bi-weekly [WorkflowHub Club](/project/community) c See the list of club members on the [acknowledgement](/project/acknowledgements) page. +### Contact Us + +The production instance is hosted by [eScience Lab](https://esciencelab.org.uk/) at [The University of Manchester](https://www.manchester.ac.uk/) led by professor [Carole Goble](https://research.manchester.ac.uk/en/persons/carole.goble). + +* [Provide feedback or ask question](https://workflowhub.eu/home/feedback) +* Contribute to [WorkflowHub club](https://about.workflowhub.eu/project/community/) (Regular telcons, Slack chat, public mailing list) +* [Report an issue](https://workflowhub.eu/home/report_issue) (public GitHub), or: + - Contact `workflowhub.eu` system administrators: + - Report [Code of Conduct](https://github.com/workflowhub-eu/about/blob/master/CODE_OF_CONDUCT.md) concerns: +* Academic collaborations: + + +## WfCommons and WorkflowHub + +Note that the US-based [WfCommons](https://wfcommons.org/), a Python-based framework for enabling scientific workflow research and development, was previously [called "WorkflowHub"](https://doi.org/10.1109/WORKS51914.2020.00012). While that framework is not related to our registry workflowhub.eu, this name collision could cause some confusion, so in common agreement with Rafael Ferreira da Silva, their former domain name `workflowhub.org` +now kindly redirect to our workflow registry , their framework was renamed to "WfCommons" and moved to and their Python package `workflowhub` was renamed [`wfcommons`](https://pypi.org/project/wfcommons/). + ## Code of conduct This project has a [Code of Conduct](https://github.com/workflowhub-eu/about/blob/master/CODE_OF_CONDUCT.md) to ensure interactions are friendly, respectful and inclusive. You can contact if you have any concerns or questions. -## Citation +## Retention and End-of-Life policy -{% include citation.md %} +WorkflowHub's sustainability plan is to ensure the availability of its contributions and metadata up to and beyond 2027. If and when the WorkflowHub reaches its end of service after that, the published contributions and metadata will be archived as RO-Crates and made available through a public repository, such as Zenodo, Figshare or another appropriate resource at that time. [DOI registrations](/docs/citable/) will in this case be updated to link to the archived deposits. ## Acknowledgements @@ -83,9 +107,7 @@ We are grateful for contributions from [**EOSC-Life**](https://www.eosc-life.eu -## Retention and End-of-Life policy -WorkflowHub's sustainability plan is to ensure the availability of its contributions and metadata up to and beyond 2027. If and when the WorkflowHub reaches its end of service after that, the published contributions and metadata will be archived as RO-Crates and made available through a public repository, such as Zenodo, Figshare or another appropriate resource at that time. [DOI registrations](/docs/citable/) will in this case be updated to link to the archived deposits. * [WorkflowHub](https://workflowhub.eu) is a domain-agnostic workflow registry designed around [FAIR principles](https://workflows.community/groups/fair/). @@ -100,24 +122,6 @@ WorkflowHub's sustainability plan is to ensure the availability of its contribut * The [WorkflowHub Club](/project/community/) open community works together to continuously co-develop the Hub. * First beta-released in Sept 2020 and production-released in September 2022, the Hub now holds over [300 workflows](https://workflowhub.eu/workflows), including 49 curated [COVID-19 workflows](https://covid19.workflowhub.eu/). It is a listed resource of the European [COVID19 Data Portal](https://www.covid19dataportal.org/) and as a [EOSC Data Source](https://marketplace.eosc-portal.eu/datasources/eosc.elixir-uk.5126ffcc8e23f65bbbe219d36128f2c8). -## Contact Us - -The production instance is hosted by [eScience Lab](https://esciencelab.org.uk/) at [The University of Manchester](https://www.manchester.ac.uk/) led by professor [Carole Goble](https://research.manchester.ac.uk/en/persons/carole.goble). - -* [Provide feedback or ask question](https://workflowhub.eu/home/feedback) -* Contribute to [WorkflowHub club](https://about.workflowhub.eu/project/community/) (Regular telcons, Slack chat, public mailing list) -* [Report an issue](https://workflowhub.eu/home/report_issue) (public GitHub), or: - - Contact `workflowhub.eu` system administrators: - - Report [Code of Conduct](https://github.com/workflowhub-eu/about/blob/master/CODE_OF_CONDUCT.md) concerns: -* Academic collaborations: - - -## WfCommons and WorkflowHub - -Note that the US-based [WfCommons](https://wfcommons.org/), a Python-based framework for enabling scientific workflow research and development, was previously [called "WorkflowHub"](https://doi.org/10.1109/WORKS51914.2020.00012). While that framework is not related to our registry workflowhub.eu, this name collision could cause some confusion, so in common agreement with Rafael Ferreira da Silva, their former domain name `workflowhub.org` -now kindly redirect to our workflow registry , their framework was renamed to "WfCommons" and moved to and their Python package `workflowhub` was renamed [`wfcommons`](https://pypi.org/project/wfcommons/). - - ## Development From 6eb2313eb8848e59fb602418887db9c27a196dbe Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 31 Oct 2024 11:05:44 +1030 Subject: [PATCH 08/31] New structure for index.md --- index.md | 46 +++++++++++++++++++++++++--------------------- 1 file changed, 25 insertions(+), 21 deletions(-) diff --git a/index.md b/index.md index d2e72f1..a3cf335 100644 --- a/index.md +++ b/index.md @@ -19,6 +19,18 @@ For more details, see [About WorkflowHub](project), [FAIR Computational Workflow For any kind of questions or suggestions on using WorkflowHub, feel free to join our [community](/project/community)! +* [WorkflowHub](https://workflowhub.eu) is a domain-agnostic workflow registry designed around [FAIR principles](https://workflows.community/groups/fair/). +* WorkflowHub allows workflows to be FAIR, citable, have managed *metadata* profiles, and be openly available for review and analytics. +* Workflows are packaged, registered, downloaded and exchanged as [workflow-centric Research Objects](/Workflow-RO-Crate/) using the [RO-Crate](https://w3id.org/ro/crate) specification, with test and example data, managed metadata profiles, citations and more. +* A [schema.org](https://schema.org/) based Bioschemas profile describes the metadata about a workflow and use of the [Common Workflow Language](https://www.commonwl.org/) is encouraged, providing a canonical description of the workflow itself. +* Popular workflow management systems such as [Galaxy](https://galaxyproject.org/), [Nextflow](https://nextflow.io/), and [Snakemake](https://snakemake.readthedocs.io/) are working with the Hub to seamlessly and automatically support object packaging, registration and exchange. +* WorkflowHub is *workflow management system agnostic*: workflows may remain in their native repositories in their native forms. +* WorkflowHub provides features such as community spaces, collections, versioning and snapshots, and contributor credit. +* In addition to its own [APIs](https://workflowhub.eu/api), WorkflowHub supports community registry standards and services such as [GA4GH TRS](https://about.workflowhub.eu/TRS/) and [ELIXIR-AAI](https://elixir-europe.org/services/compute/aai) authentication, and current work integrates with the [LifeMonitor workflow testing](https://lifemonitor.eu/) service. +* WorkflowHub is mainly sponsored by the European RI Cluster [EOSC-Life](https://www.eosc-life.eu/), the European Research Infrastructure [ELIXIR](https://elixir-europe.org/) and [EuroScienceGateway](http://eurosciencegateway.eu/) (see [full list of acknowledgements](/project/acknowledgements/#funding)). +* The [WorkflowHub Club](/project/community/) open community works together to continuously co-develop the Hub. +* First beta-released in Sept 2020 and production-released in September 2022, the Hub now holds over [300 workflows](https://workflowhub.eu/workflows), including 49 curated [COVID-19 workflows](https://covid19.workflowhub.eu/). It is a listed resource of the European [COVID19 Data Portal](https://www.covid19dataportal.org/) and as a [EOSC Data Source](https://marketplace.eosc-portal.eu/datasources/eosc.elixir-uk.5126ffcc8e23f65bbbe219d36128f2c8). + ## Documentation @@ -72,6 +84,19 @@ Anyone is welcome to join the bi-weekly [WorkflowHub Club](/project/community) c See the list of club members on the [acknowledgement](/project/acknowledgements) page. +### Development + +Created as part of the [EOSC-Life](https://www.eosc-life.eu) WP2 [Tools Collaboratory](https://github.com/eosc-life/tools-collaboratory-roadmap), WorkflowHub is in production but still under active development. + +See a complete list of contributors on the [acknowledgement](/project/acknowledgements) page. + +Aims of the project include: + +* Evolvement of [myExperiment](https://myexperiment.org/) that is workflow system agnostic, supports a repository of workflows in native and standardised form (e.g. [CWL](https://www.commonwl.org/) and the virtual aggregation of established tool, workflow and registries to support discovery over a fragmented ecosystem. The federated registry would support a **common API** to simplify access for tool developers. +* Standardised workflow identifiers and metadata descriptions needed for workflow discovery, reuse, preservation, interoperability and monitoring and metadata harvesting using standard protocols. Workflows are usually multi-component (requiring links to test data, example runs, explanatory documentation, etc) and used in collections for scientific use cases. We plan to use the Research Object specification for packaging workflows, which has already been combined with [CWL](https://www.commonwl.org/) and is part of the [BioComputeObject](http://biocomputeobject.org/) specification. +* Workflow snapshot preservation, publishing, citation and monitoring, credit claiming and workflows part of the scholarly communication landscape partnering with platforms like [DataCite](https://datacite.org/) and EOSC’s [OpenAIRE](https://www.openaire.eu/) and their Research Community Dashboards linking publications with workflows, associated datasets, software, etc. +* The workflow registry is planned to be based on the [SEEK platform](https://seek4science.org/) using [Common Workflow Language](https://www.commonwl.org/) and [Research Objects](http://www.researchobject.org/) to glue in federated workflow and tool descriptions across the research infrastructures. + ### Contact Us The production instance is hosted by [eScience Lab](https://esciencelab.org.uk/) at [The University of Manchester](https://www.manchester.ac.uk/) led by professor [Carole Goble](https://research.manchester.ac.uk/en/persons/carole.goble). @@ -110,28 +135,7 @@ We are grateful for contributions from [**EOSC-Life**](https://www.eosc-life.eu -* [WorkflowHub](https://workflowhub.eu) is a domain-agnostic workflow registry designed around [FAIR principles](https://workflows.community/groups/fair/). -* WorkflowHub allows workflows to be FAIR, citable, have managed *metadata* profiles, and be openly available for review and analytics. -* Workflows are packaged, registered, downloaded and exchanged as [workflow-centric Research Objects](/Workflow-RO-Crate/) using the [RO-Crate](https://w3id.org/ro/crate) specification, with test and example data, managed metadata profiles, citations and more. -* A [schema.org](https://schema.org/) based Bioschemas profile describes the metadata about a workflow and use of the [Common Workflow Language](https://www.commonwl.org/) is encouraged, providing a canonical description of the workflow itself. -* Popular workflow management systems such as [Galaxy](https://galaxyproject.org/), [Nextflow](https://nextflow.io/), and [Snakemake](https://snakemake.readthedocs.io/) are working with the Hub to seamlessly and automatically support object packaging, registration and exchange. -* WorkflowHub is *workflow management system agnostic*: workflows may remain in their native repositories in their native forms. -* WorkflowHub provides features such as community spaces, collections, versioning and snapshots, and contributor credit. -* In addition to its own [APIs](https://workflowhub.eu/api), WorkflowHub supports community registry standards and services such as [GA4GH TRS](https://about.workflowhub.eu/TRS/) and [ELIXIR-AAI](https://elixir-europe.org/services/compute/aai) authentication, and current work integrates with the [LifeMonitor workflow testing](https://lifemonitor.eu/) service. -* WorkflowHub is mainly sponsored by the European RI Cluster [EOSC-Life](https://www.eosc-life.eu/), the European Research Infrastructure [ELIXIR](https://elixir-europe.org/) and [EuroScienceGateway](http://eurosciencegateway.eu/) (see [full list of acknowledgements](/project/acknowledgements/#funding)). -* The [WorkflowHub Club](/project/community/) open community works together to continuously co-develop the Hub. -* First beta-released in Sept 2020 and production-released in September 2022, the Hub now holds over [300 workflows](https://workflowhub.eu/workflows), including 49 curated [COVID-19 workflows](https://covid19.workflowhub.eu/). It is a listed resource of the European [COVID19 Data Portal](https://www.covid19dataportal.org/) and as a [EOSC Data Source](https://marketplace.eosc-portal.eu/datasources/eosc.elixir-uk.5126ffcc8e23f65bbbe219d36128f2c8). - - -## Development -Created as part of the [EOSC-Life](https://www.eosc-life.eu) WP2 [Tools Collaboratory](https://github.com/eosc-life/tools-collaboratory-roadmap), WorkflowHub is in production but still under active development. -See a complete list of contributors on the [acknowledgement](/project/acknowledgements) page. -Aims of the project include: -* Evolvement of [myExperiment](https://myexperiment.org/) that is workflow system agnostic, supports a repository of workflows in native and standardised form (e.g. [CWL](https://www.commonwl.org/) and the virtual aggregation of established tool, workflow and registries to support discovery over a fragmented ecosystem. The federated registry would support a **common API** to simplify access for tool developers. -* Standardised workflow identifiers and metadata descriptions needed for workflow discovery, reuse, preservation, interoperability and monitoring and metadata harvesting using standard protocols. Workflows are usually multi-component (requiring links to test data, example runs, explanatory documentation, etc) and used in collections for scientific use cases. We plan to use the Research Object specification for packaging workflows, which has already been combined with [CWL](https://www.commonwl.org/) and is part of the [BioComputeObject](http://biocomputeobject.org/) specification. -* Workflow snapshot preservation, publishing, citation and monitoring, credit claiming and workflows part of the scholarly communication landscape partnering with platforms like [DataCite](https://datacite.org/) and EOSC’s [OpenAIRE](https://www.openaire.eu/) and their Research Community Dashboards linking publications with workflows, associated datasets, software, etc. -* The workflow registry is planned to be based on the [SEEK platform](https://seek4science.org/) using [Common Workflow Language](https://www.commonwl.org/) and [Research Objects](http://www.researchobject.org/) to glue in federated workflow and tool descriptions across the research infrastructures. From da88a46bbc8e15a75f5bf8e94aa50b2d55a35fb8 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 31 Oct 2024 11:19:14 +1030 Subject: [PATCH 09/31] New structure for index.md --- index.md | 35 +++++++++++++---------------------- 1 file changed, 13 insertions(+), 22 deletions(-) diff --git a/index.md b/index.md index a3cf335..9aec70c 100644 --- a/index.md +++ b/index.md @@ -7,19 +7,11 @@ hide_sidebar: true sidebar: true --- -[WorkflowHub](https://workflowhub.eu/) is a FAIR registry for describing, sharing and publishing scientific computational workflows. The registry is sponsored by the European RI Cluster EOSC-Life, the European Research Infrastructure ELIXIR, and [multiple EU-wide projects](/project/acknowledgements/#funding). - -It is workflow management system agnostic: workflows may remain in their native repositories in their native forms. +[WorkflowHub](https://workflowhub.eu/) is a FAIR registry for describing, sharing and publishing scientific computational workflows. The registry is sponsored by the European RI Cluster EOSC-Life, the European Research Infrastructure ELIXIR, and [multiple EU-wide projects](/project/acknowledgements/#funding). This website describes the open source **project** for developing and running [WorkflowHub](https://workflowhub.eu/). -{% include section-navigation-tiles.html col = "2" custom="news, outreach, docs" sort=false %} - -For more details, see [About WorkflowHub](project), [FAIR Computational Workflows](https://workflows.community/groups/fair/), [Outreach and Publications](project/outreach). - -For any kind of questions or suggestions on using WorkflowHub, feel free to join our [community](/project/community)! - -* [WorkflowHub](https://workflowhub.eu) is a domain-agnostic workflow registry designed around [FAIR principles](https://workflows.community/groups/fair/). +* [WorkflowHub](https://workflowhub.eu) is a domain-agnostic workflow registry designed around [FAIR principles](https://workflows.community/groups/fair/). It is also workflow management system agnostic: workflows may remain in their native repositories in their native forms. * WorkflowHub allows workflows to be FAIR, citable, have managed *metadata* profiles, and be openly available for review and analytics. * Workflows are packaged, registered, downloaded and exchanged as [workflow-centric Research Objects](/Workflow-RO-Crate/) using the [RO-Crate](https://w3id.org/ro/crate) specification, with test and example data, managed metadata profiles, citations and more. * A [schema.org](https://schema.org/) based Bioschemas profile describes the metadata about a workflow and use of the [Common Workflow Language](https://www.commonwl.org/) is encouraged, providing a canonical description of the workflow itself. @@ -31,19 +23,23 @@ For any kind of questions or suggestions on using WorkflowHub, feel free to join * The [WorkflowHub Club](/project/community/) open community works together to continuously co-develop the Hub. * First beta-released in Sept 2020 and production-released in September 2022, the Hub now holds over [300 workflows](https://workflowhub.eu/workflows), including 49 curated [COVID-19 workflows](https://covid19.workflowhub.eu/). It is a listed resource of the European [COVID19 Data Portal](https://www.covid19dataportal.org/) and as a [EOSC Data Source](https://marketplace.eosc-portal.eu/datasources/eosc.elixir-uk.5126ffcc8e23f65bbbe219d36128f2c8). +For more details, see [FAIR Computational Workflows](https://workflows.community/groups/fair/), [Outreach and Publications](project/outreach). -## Documentation +For any kind of questions or suggestions on using WorkflowHub, feel free to join our [community](#community)! -* [Documentation & Quick Start guide](docs/) (See also _Detailed Documentation_) -* [Guide to using WorkflowHub](docs/guide-to-using-workflowhub/) -* [Developer docs](developer/) -* Tutorial vidoes: - - [Make your workflows findable and citable](https://www.youtube.com/watch?v=2kGKxaPuQN8) ([slides](https://doi.org/10.5281/zenodo.7787488)) - - [WorkflowHub ask-me-anything](https://workflowhub.eu/presentations/19?version=1) tutorial session + +## Citation + +{% include citation.md %} ## Project resources +{% include section-navigation-tiles.html col = "2" custom="news, outreach, docs" sort=false %} + +* **Tutorial videos:** + - [Make your workflows findable and citable](https://www.youtube.com/watch?v=2kGKxaPuQN8) ([slides](https://doi.org/10.5281/zenodo.7787488)) + - [WorkflowHub ask-me-anything](https://workflowhub.eu/presentations/19?version=1) tutorial session * **Production instance**: * **Sandbox instance**: (use for testing; occasionally wiped) * **Source code**: [seek4science/seek](https://github.com/seek4science/seek) @@ -66,11 +62,6 @@ For any kind of questions or suggestions on using WorkflowHub, feel free to join * [WorkflowHub Introduction slides](https://drive.google.com/open?id=1hfBAjjRnL9jGoxHEvq66Wo-wuKqouR3C). Carole Goble, 2020-03-25 -## Citation - -{% include citation.md %} - - ## Get involved ### Community From a1eff9fe365e425ded5064a066e0cd55bf712987 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 31 Oct 2024 11:20:45 +1030 Subject: [PATCH 10/31] New structure for index.md --- index.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/index.md b/index.md index 9aec70c..14021d0 100644 --- a/index.md +++ b/index.md @@ -38,8 +38,8 @@ For any kind of questions or suggestions on using WorkflowHub, feel free to join {% include section-navigation-tiles.html col = "2" custom="news, outreach, docs" sort=false %} * **Tutorial videos:** - - [Make your workflows findable and citable](https://www.youtube.com/watch?v=2kGKxaPuQN8) ([slides](https://doi.org/10.5281/zenodo.7787488)) - - [WorkflowHub ask-me-anything](https://workflowhub.eu/presentations/19?version=1) tutorial session + * [Make your workflows findable and citable](https://www.youtube.com/watch?v=2kGKxaPuQN8) ([slides](https://doi.org/10.5281/zenodo.7787488)) + * [WorkflowHub ask-me-anything](https://workflowhub.eu/presentations/19?version=1) tutorial session * **Production instance**: * **Sandbox instance**: (use for testing; occasionally wiped) * **Source code**: [seek4science/seek](https://github.com/seek4science/seek) From 5fb583ecd9dc948a7442128dcfd017649ca6a2b7 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 31 Oct 2024 11:38:13 +1030 Subject: [PATCH 11/31] New structure for index.md --- _data/topnav.yml | 4 +--- index.md | 20 +++++++++++++------- 2 files changed, 14 insertions(+), 10 deletions(-) diff --git a/_data/topnav.yml b/_data/topnav.yml index ded7827..d5605eb 100644 --- a/_data/topnav.yml +++ b/_data/topnav.yml @@ -1,9 +1,7 @@ ## Topnav single links ## if you want to list an external url, use external_url instead of url. the theme will apply a different link base. subitems: - - title: Home - url: / - title: About - url: /project/ + url: / - title: Documentation url: /docs/ diff --git a/index.md b/index.md index 14021d0..d231c77 100644 --- a/index.md +++ b/index.md @@ -1,6 +1,6 @@ --- title: WorkflowHub project -toc: false +toc: true permalink: / # There are special sidebar rules for the index page in layouts/default.html hide_sidebar: true @@ -11,23 +11,30 @@ sidebar: true This website describes the open source **project** for developing and running [WorkflowHub](https://workflowhub.eu/). -* [WorkflowHub](https://workflowhub.eu) is a domain-agnostic workflow registry designed around [FAIR principles](https://workflows.community/groups/fair/). It is also workflow management system agnostic: workflows may remain in their native repositories in their native forms. +* [WorkflowHub](https://workflowhub.eu) is a domain-agnostic workflow registry designed around [FAIR principles](https://workflows.community/groups/fair/). +* WorkflowHub is *workflow management system agnostic*: workflows may remain in their native repositories in their native forms. +* WorkflowHub provides features such as community spaces, collections, versioning and snapshots, and contributor credit. * WorkflowHub allows workflows to be FAIR, citable, have managed *metadata* profiles, and be openly available for review and analytics. * Workflows are packaged, registered, downloaded and exchanged as [workflow-centric Research Objects](/Workflow-RO-Crate/) using the [RO-Crate](https://w3id.org/ro/crate) specification, with test and example data, managed metadata profiles, citations and more. * A [schema.org](https://schema.org/) based Bioschemas profile describes the metadata about a workflow and use of the [Common Workflow Language](https://www.commonwl.org/) is encouraged, providing a canonical description of the workflow itself. -* Popular workflow management systems such as [Galaxy](https://galaxyproject.org/), [Nextflow](https://nextflow.io/), and [Snakemake](https://snakemake.readthedocs.io/) are working with the Hub to seamlessly and automatically support object packaging, registration and exchange. -* WorkflowHub is *workflow management system agnostic*: workflows may remain in their native repositories in their native forms. -* WorkflowHub provides features such as community spaces, collections, versioning and snapshots, and contributor credit. +* Popular workflow management systems such as [Galaxy](https://galaxyproject.org/), [Nextflow](https://nextflow.io/), and [Snakemake](https://snakemake.readthedocs.io/) are working with the Hub to seamlessly and automatically support object packaging, registration and exchange. * In addition to its own [APIs](https://workflowhub.eu/api), WorkflowHub supports community registry standards and services such as [GA4GH TRS](https://about.workflowhub.eu/TRS/) and [ELIXIR-AAI](https://elixir-europe.org/services/compute/aai) authentication, and current work integrates with the [LifeMonitor workflow testing](https://lifemonitor.eu/) service. * WorkflowHub is mainly sponsored by the European RI Cluster [EOSC-Life](https://www.eosc-life.eu/), the European Research Infrastructure [ELIXIR](https://elixir-europe.org/) and [EuroScienceGateway](http://eurosciencegateway.eu/) (see [full list of acknowledgements](/project/acknowledgements/#funding)). * The [WorkflowHub Club](/project/community/) open community works together to continuously co-develop the Hub. -* First beta-released in Sept 2020 and production-released in September 2022, the Hub now holds over [300 workflows](https://workflowhub.eu/workflows), including 49 curated [COVID-19 workflows](https://covid19.workflowhub.eu/). It is a listed resource of the European [COVID19 Data Portal](https://www.covid19dataportal.org/) and as a [EOSC Data Source](https://marketplace.eosc-portal.eu/datasources/eosc.elixir-uk.5126ffcc8e23f65bbbe219d36128f2c8). For more details, see [FAIR Computational Workflows](https://workflows.community/groups/fair/), [Outreach and Publications](project/outreach). For any kind of questions or suggestions on using WorkflowHub, feel free to join our [community](#community)! +## Did you know? + +* The first beta-release was in Sept 2020, +* Production-release was in September 2022, +* The WorkflowHub now holds over [300 workflows](https://workflowhub.eu/workflows), including 49 curated [COVID-19 workflows](https://covid19.workflowhub.eu/), +* It is a listed resource of the European [COVID19 Data Portal](https://www.covid19dataportal.org/), and is a [EOSC Data Source](https://marketplace.eosc-portal.eu/datasources/eosc.elixir-uk.5126ffcc8e23f65bbbe219d36128f2c8). + + ## Citation {% include citation.md %} @@ -44,7 +51,6 @@ For any kind of questions or suggestions on using WorkflowHub, feel free to join * **Sandbox instance**: (use for testing; occasionally wiped) * **Source code**: [seek4science/seek](https://github.com/seek4science/seek) * **API documentation**: -* **[Outreach and Publications](/project/outreach/)** * **EOSC-Life Deliverable 2.3**: * **Tasks**: * [WorkflowHub roadmap](/project/roadmap) (deprecated -- now managed in Trello) From d85cb0ebbc5a53b909897ea3d44f704ff43dfc98 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 31 Oct 2024 11:40:57 +1030 Subject: [PATCH 12/31] New structure for index.md --- index.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/index.md b/index.md index d231c77..2768d65 100644 --- a/index.md +++ b/index.md @@ -7,6 +7,8 @@ hide_sidebar: true sidebar: true --- +## About + [WorkflowHub](https://workflowhub.eu/) is a FAIR registry for describing, sharing and publishing scientific computational workflows. The registry is sponsored by the European RI Cluster EOSC-Life, the European Research Infrastructure ELIXIR, and [multiple EU-wide projects](/project/acknowledgements/#funding). This website describes the open source **project** for developing and running [WorkflowHub](https://workflowhub.eu/). From 2d19cd31d445b1e42fec70f0d3c7e465f8aa6483 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 31 Oct 2024 12:57:34 +1030 Subject: [PATCH 13/31] Merge content and add links to index.md --- _data/CONTRIBUTORS.yaml | 24 +++++++++++++++++++++++- index.md | 31 ++++++++++++++++++++----------- project/community.md | 33 --------------------------------- project/events.md | 1 + project/roadmap.md | 1 + 5 files changed, 45 insertions(+), 45 deletions(-) diff --git a/_data/CONTRIBUTORS.yaml b/_data/CONTRIBUTORS.yaml index a3096ae..eb9a469 100644 --- a/_data/CONTRIBUTORS.yaml +++ b/_data/CONTRIBUTORS.yaml @@ -5,4 +5,26 @@ Bert Droesbeke: git: bedroesb email: bedro@psb.ugent.be - orcid: 0000-0003-0522-5674 \ No newline at end of file + orcid: 0000-0003-0522-5674 + +Johan Gustafsson: + git: supernord + orcid: 0000-0002-2977-5032 + role: product owner + affiliation: Australian BioCommons / University of Melbourne + +Frederik Coppens: + git: frederikcoppens + role: product owner + affiliation: VIB + +Carole Goble: + git: CaroleGoble + orcid: 0000-0003-1219-2137 + role: product owner + affiliation: University of Manchester + +Finn Bacall: + git: fbacall + role: lead developer + affiliation: University of Manchester diff --git a/index.md b/index.md index 2768d65..204dd22 100644 --- a/index.md +++ b/index.md @@ -44,7 +44,7 @@ For any kind of questions or suggestions on using WorkflowHub, feel free to join ## Project resources -{% include section-navigation-tiles.html col = "2" custom="news, outreach, docs" sort=false %} +{% include section-navigation-tiles.html col = "2" custom="events, news, outreach, docs, roadmap" sort=false %} * **Tutorial videos:** * [Make your workflows findable and citable](https://www.youtube.com/watch?v=2kGKxaPuQN8) ([slides](https://doi.org/10.5281/zenodo.7787488)) @@ -55,13 +55,8 @@ For any kind of questions or suggestions on using WorkflowHub, feel free to join * **API documentation**: * **EOSC-Life Deliverable 2.3**: * **Tasks**: - * [WorkflowHub roadmap](/project/roadmap) (deprecated -- now managed in Trello) * WorkflowHub implementation (SEEK) * General WorkflowHub -* **Mailing list**: [`workflowhub😊elixir-europe.org`](https://lists.elixir-europe.org/mailman/listinfo/workflowhub_elixir-europe.org) ([subscribe](https://lists.elixir-europe.org/mailman/listinfo/workflowhub_elixir-europe.org)/[archive](https://mail.elixir-europe.org/pipermail/workflowhub_elixir-europe.org/)) -* **Slack chat**: [#workflows on seek4science.slack.com](https://seek4science.slack.com/archives/CPLLVV94L) ([join](https://join.slack.com/t/seek4science/shared_invite/zt-csqh94qb-kf~kFbZxuHl1Hpxhbc8avw)) -* [Google Drive](https://drive.google.com/drive/folders/1_bZ63W4oRtWL5OnWJNYvE4u3A27VyGGe) - (to request write-access, ask in Slack channel) * **Slides/posters** (for complete list, see [Outreach](/project/outreach/)): * [WorkflowHub: FAIR Workflow Registry](https://doi.org/10.5281/zenodo.7323471). Justin Clark-Casey et al, EOSC Symposium 2022, 2022-11-14 * [WorkflowHub – a FAIR registry for workflows](https://doi.org/10.7490/f1000research.1118984.1). Carole Goble, ELIXIR All Hands 2022 @@ -72,16 +67,24 @@ For any kind of questions or suggestions on using WorkflowHub, feel free to join ## Get involved + ### Community -Regular meeting: **WorkflowHub Club** - all welcome! +While WorkflowHub is largely developed as a collaboration between [several projects](/project/acknowledgements), any contributors are welcome to join our **open community**. + +Anyone can [join the WorkflowHub club](https://github.com/workflowhub-eu/about/issues/1)! Either sign up on GitHub [issue #1](https://github.com/workflowhub-eu/about/issues/1) or join the [next bi-weekly Zoom call](https://s.apache.org/workflowhub-minutes) and introduce yourself. + +* **When:** Alternate Wednesdays 10:00 current UK time zone / 11:00 current Central European time zone +* **Agenda, telcon details and minutes:** + +See the list of WorkflowHub Club members on the [acknowledgements page](/project/acknowledgements). -Anyone is welcome to join the bi-weekly [WorkflowHub Club](/project/community) calls using Zoom. +For asynchronous communication, see also: -* When: Alternate Wednesdays 10:00 current UK time zone / 11:00 current Central European time zone -* Agenda, telcon details and minutes: +* **Mailing list**: [`workflowhub😊elixir-europe.org`](https://lists.elixir-europe.org/mailman/listinfo/workflowhub_elixir-europe.org) ([subscribe](https://lists.elixir-europe.org/mailman/listinfo/workflowhub_elixir-europe.org)/[archive](https://mail.elixir-europe.org/pipermail/workflowhub_elixir-europe.org/)) +* **Slack chat**: [#workflows on seek4science.slack.com](https://seek4science.slack.com/archives/CPLLVV94L) ([join](https://join.slack.com/t/seek4science/shared_invite/zt-csqh94qb-kf~kFbZxuHl1Hpxhbc8avw)) +* [Google Drive](https://drive.google.com/drive/folders/1_bZ63W4oRtWL5OnWJNYvE4u3A27VyGGe): to request write-access, ask in Slack channel -See the list of club members on the [acknowledgement](/project/acknowledgements) page. ### Development @@ -96,6 +99,7 @@ Aims of the project include: * Workflow snapshot preservation, publishing, citation and monitoring, credit claiming and workflows part of the scholarly communication landscape partnering with platforms like [DataCite](https://datacite.org/) and EOSC’s [OpenAIRE](https://www.openaire.eu/) and their Research Community Dashboards linking publications with workflows, associated datasets, software, etc. * The workflow registry is planned to be based on the [SEEK platform](https://seek4science.org/) using [Common Workflow Language](https://www.commonwl.org/) and [Research Objects](http://www.researchobject.org/) to glue in federated workflow and tool descriptions across the research infrastructures. + ### Contact Us The production instance is hosted by [eScience Lab](https://esciencelab.org.uk/) at [The University of Manchester](https://www.manchester.ac.uk/) led by professor [Carole Goble](https://research.manchester.ac.uk/en/persons/carole.goble). @@ -124,6 +128,11 @@ This project has a [Code of Conduct](https://github.com/workflowhub-eu/about/blo WorkflowHub's sustainability plan is to ensure the availability of its contributions and metadata up to and beyond 2027. If and when the WorkflowHub reaches its end of service after that, the published contributions and metadata will be archived as RO-Crates and made available through a public repository, such as Zenodo, Figshare or another appropriate resource at that time. [DOI registrations](/docs/citable/) will in this case be updated to link to the archived deposits. +## Governance + +{% include contributor-tiles-all.html custom="Johan Gustafsson, Frederik Coppens, Carole Goble" %} + + ## Acknowledgements We are grateful for contributions from [**EOSC-Life**](https://www.eosc-life.eu/), [ELIXIR Europe](https://elixir-europe.org/), [**EuroScienceGateway**](http://eurosciencegateway.eu/) and others (see complete [list of funders](/project/acknowledgements#funding)). diff --git a/project/community.md b/project/community.md index 93d15ec..a761248 100644 --- a/project/community.md +++ b/project/community.md @@ -3,36 +3,3 @@ title: WorkflowHub community --- -While WorkflowHub is largely developed as a collaboration between [several projects](/project/acknowledgements), any contributors are welcome to join our **open community**. - - -## WorkflowHub Club - -[WorkflowHub Club](https://s.apache.org/workflowhub-minutes): - -* **Schedule**: Bi-weekly, Wednesday 10:00 BST / 11:00 CEST -* **Agenda / call details**: - -Anyone can [join the WorkflowHub club](https://github.com/workflowhub-eu/about/issues/1)! Either sign up on GitHub [issue #1](https://github.com/workflowhub-eu/about/issues/1) or join the [next call](https://s.apache.org/workflowhub-minutes) and introduce yourself. - -See [acknowledgements](/project/acknowledgements#workflowhub-club) for a complete list of participants in the WorkflowHub Club. - -For asynchronous communication, see also: - -* **Mailing list**: [`workflowhub😊elixir-europe.org`](https://lists.elixir-europe.org/mailman/listinfo/workflowhub_elixir-europe.org) ([subscribe](https://lists.elixir-europe.org/mailman/listinfo/workflowhub_elixir-europe.org)/[archive](https://mail.elixir-europe.org/pipermail/workflowhub_elixir-europe.org/)) -* **Slack chat**: [#workflows on seek4science.slack.com](https://seek4science.slack.com/archives/CPLLVV94L) ([join](https://join.slack.com/t/seek4science/shared_invite/zt-csqh94qb-kf~kFbZxuHl1Hpxhbc8avw)) -* [Google Drive](https://drive.google.com/drive/folders/1_bZ63W4oRtWL5OnWJNYvE4u3A27VyGGe) - (to request write-access, ask in Slack channel) - -### Governance - -Product Owners: - -* Johan Gustafsson, Australian Biocommons -* Carole Goble, The University of Manchester -* Frederik Coppens, VIB - - -## Code of conduct - -This project has a [Code of Conduct](https://github.com/workflowhub-eu/about/blob/master/CODE_OF_CONDUCT.md) to ensure interactions are friendly, respectful and inclusive. You can contact if you have any concerns or questions. diff --git a/project/events.md b/project/events.md index cb69efd..ac1d4c0 100644 --- a/project/events.md +++ b/project/events.md @@ -1,5 +1,6 @@ --- title: Events +page_id: events --- diff --git a/project/roadmap.md b/project/roadmap.md index 887a5c2..6ec5249 100644 --- a/project/roadmap.md +++ b/project/roadmap.md @@ -1,5 +1,6 @@ --- title: Roadmap +page_id: roadmap redirect_from: /roadmap/ --- From 0c2837280f9c7edce9829d80fd4f1abab89660b7 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 31 Oct 2024 13:03:46 +1030 Subject: [PATCH 14/31] Update tiles for index.md --- index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.md b/index.md index 204dd22..67a0931 100644 --- a/index.md +++ b/index.md @@ -44,7 +44,7 @@ For any kind of questions or suggestions on using WorkflowHub, feel free to join ## Project resources -{% include section-navigation-tiles.html col = "2" custom="events, news, outreach, docs, roadmap" sort=false %} +{% include section-navigation-tiles.html col = "3" custom="outreach, docs, roadmap" sort=false %} * **Tutorial videos:** * [Make your workflows findable and citable](https://www.youtube.com/watch?v=2kGKxaPuQN8) ([slides](https://doi.org/10.5281/zenodo.7787488)) From a77e7a08a3e8c117da14599f62be99a59d919b82 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 31 Oct 2024 13:11:45 +1030 Subject: [PATCH 15/31] Updates for index.md --- _includes/citation.md | 2 +- index.md | 2 +- project/acknowledgements.md | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/_includes/citation.md b/_includes/citation.md index 84d6cac..f5e2b52 100644 --- a/_includes/citation.md +++ b/_includes/citation.md @@ -5,5 +5,5 @@ Ove Johan Ragnar Gustafsson, Sean R. Wilkinson, Finn Bacall, Stian Soiland-Reyes _arXiv_:2410.06941 [cs.DL] +{% include callout.html type="tip" content="See also [publication and outreach](/project/outreach) for more specific work." %} -See also [publication and outreach](/project/outreach) for more specific work. diff --git a/index.md b/index.md index 67a0931..9fc9861 100644 --- a/index.md +++ b/index.md @@ -33,7 +33,7 @@ For any kind of questions or suggestions on using WorkflowHub, feel free to join * The first beta-release was in Sept 2020, * Production-release was in September 2022, -* The WorkflowHub now holds over [300 workflows](https://workflowhub.eu/workflows), including 49 curated [COVID-19 workflows](https://covid19.workflowhub.eu/), +* The WorkflowHub now holds over [700 workflows](https://workflowhub.eu/workflows), including 49 curated [COVID-19 workflows](https://covid19.workflowhub.eu/), * It is a listed resource of the European [COVID19 Data Portal](https://www.covid19dataportal.org/), and is a [EOSC Data Source](https://marketplace.eosc-portal.eu/datasources/eosc.elixir-uk.5126ffcc8e23f65bbbe219d36128f2c8). diff --git a/project/acknowledgements.md b/project/acknowledgements.md index e5c21ee..0248263 100644 --- a/project/acknowledgements.md +++ b/project/acknowledgements.md @@ -80,7 +80,7 @@ The WorkflowHub community collaborates closely with (at least) these projects: ## WorkflowHub Club -The weekly [WorkflowHub Club](/project/community) is chaired by **Finn Bacall**. +The weekly [WorkflowHub Club](/project/community) is chaired by **Johan Gustafsson**. Participants include: From 0e661fa4be1a2c322f17b31a87ae0d65b41023f6 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 31 Oct 2024 13:35:54 +1030 Subject: [PATCH 16/31] Remove sidebars --- index.md | 4 ++-- project/acknowledgements.md | 1 + project/outreach.md | 1 + project/roadmap.md | 1 + 4 files changed, 5 insertions(+), 2 deletions(-) diff --git a/index.md b/index.md index 9fc9861..947cfee 100644 --- a/index.md +++ b/index.md @@ -104,8 +104,8 @@ Aims of the project include: The production instance is hosted by [eScience Lab](https://esciencelab.org.uk/) at [The University of Manchester](https://www.manchester.ac.uk/) led by professor [Carole Goble](https://research.manchester.ac.uk/en/persons/carole.goble). -* [Provide feedback or ask question](https://workflowhub.eu/home/feedback) -* Contribute to [WorkflowHub club](https://about.workflowhub.eu/project/community/) (Regular telcons, Slack chat, public mailing list) +* [Provide feedback or ask questions](https://workflowhub.eu/home/feedback) +* [Contribute to WorkflowHub club](#community) * [Report an issue](https://workflowhub.eu/home/report_issue) (public GitHub), or: - Contact `workflowhub.eu` system administrators: - Report [Code of Conduct](https://github.com/workflowhub-eu/about/blob/master/CODE_OF_CONDUCT.md) concerns: diff --git a/project/acknowledgements.md b/project/acknowledgements.md index 0248263..21a7b0c 100644 --- a/project/acknowledgements.md +++ b/project/acknowledgements.md @@ -1,5 +1,6 @@ --- title: Acknowledgements +sidebar: false --- Main development, hosting and maintenance of WorkflowHub is done by the [eScience Lab](https://esciencelab.org.uk/) at The University of Manchester led by [Carole Goble](https://research.manchester.ac.uk/en/persons/carole.goble). diff --git a/project/outreach.md b/project/outreach.md index 58054ff..d6dcfbe 100644 --- a/project/outreach.md +++ b/project/outreach.md @@ -1,6 +1,7 @@ --- title: Outreach and Publications page_id: outreach +sidebar: false --- diff --git a/project/roadmap.md b/project/roadmap.md index 6ec5249..e50d705 100644 --- a/project/roadmap.md +++ b/project/roadmap.md @@ -1,6 +1,7 @@ --- title: Roadmap page_id: roadmap +sidebar: false redirect_from: /roadmap/ --- From 1e79079d0ff6dfc85675a7383cb1e780f256520e Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 4 Nov 2024 08:40:13 +1030 Subject: [PATCH 17/31] Update tiles and modify index + footer.yml content --- _data/footer.yml | 8 ++------ _includes/citation.md | 2 -- docs/index.md | 1 + index.md | 10 +++------- project/acknowledgements.md | 6 ++++++ project/citation.md | 3 +++ project/outreach.md | 7 +++++++ project/roadmap.md | 1 + 8 files changed, 23 insertions(+), 15 deletions(-) diff --git a/_data/footer.yml b/_data/footer.yml index c474c71..97c8174 100644 --- a/_data/footer.yml +++ b/_data/footer.yml @@ -1,7 +1,3 @@ -extra_line: | - ![Flag of the European Union](/assets/img/eu-flag-small.png) - [EOSC-Life](https://www.eosc-life.eu/) is funded by European Union’s Horizon 2020 programme under - grant agreement number [824087](https://doi.org/10.3030/824087) and [additional funding](/project/acknowledgements/#funding). copyright: | [about.workflowhub.eu](https://about.workflowhub.eu/) content is distributed under [BSD 3-Clause "New" or "Revised" License](https://github.com/workflowhub-eu/about/blob/master/LICENSE), @@ -10,8 +6,8 @@ columns: - type: image image_width: 120px width: 3 - src: '/assets/img/eosc-life.svg' - alt: EOSC-Life + src: '/assets/img/workflowhub-square.svg' + alt: workflowhub logo square - type: links width: 3 children: diff --git a/_includes/citation.md b/_includes/citation.md index f5e2b52..c6d4bed 100644 --- a/_includes/citation.md +++ b/_includes/citation.md @@ -5,5 +5,3 @@ Ove Johan Ragnar Gustafsson, Sean R. Wilkinson, Finn Bacall, Stian Soiland-Reyes _arXiv_:2410.06941 [cs.DL] -{% include callout.html type="tip" content="See also [publication and outreach](/project/outreach) for more specific work." %} - diff --git a/docs/index.md b/docs/index.md index 9f26c4f..fc5a29e 100644 --- a/docs/index.md +++ b/docs/index.md @@ -2,6 +2,7 @@ title: Documentation toc: false page_id: docs +type: resource redirect_from: - /docs/before-you-start/ - /docs/onboarding/ diff --git a/index.md b/index.md index 947cfee..0b044f1 100644 --- a/index.md +++ b/index.md @@ -41,10 +41,12 @@ For any kind of questions or suggestions on using WorkflowHub, feel free to join {% include citation.md %} +{% include callout.html type="tip" content="See also [publication and outreach](/project/outreach) for more specific work." %} + ## Project resources -{% include section-navigation-tiles.html col = "3" custom="outreach, docs, roadmap" sort=false %} +{% include section-navigation-tiles-simple.html col = "3" type="resource"%} * **Tutorial videos:** * [Make your workflows findable and citable](https://www.youtube.com/watch?v=2kGKxaPuQN8) ([slides](https://doi.org/10.5281/zenodo.7787488)) @@ -57,12 +59,6 @@ For any kind of questions or suggestions on using WorkflowHub, feel free to join * **Tasks**: * WorkflowHub implementation (SEEK) * General WorkflowHub -* **Slides/posters** (for complete list, see [Outreach](/project/outreach/)): - * [WorkflowHub: FAIR Workflow Registry](https://doi.org/10.5281/zenodo.7323471). Justin Clark-Casey et al, EOSC Symposium 2022, 2022-11-14 - * [WorkflowHub – a FAIR registry for workflows](https://doi.org/10.7490/f1000research.1118984.1). Carole Goble, ELIXIR All Hands 2022 - * [WorkflowHub - a registry for workflows](https://doi.org/10.5281/zenodo.4012124). Carole Goble, ECCB 2020, 2020-09-02 - * [Poster: The WorkflowHub, a registry for Life Science Workflows](https://workflowhub.eu/presentations/1). Ambarish Kumar, ISMB, 2020-07-13 - * [WorkflowHub Introduction slides](https://drive.google.com/open?id=1hfBAjjRnL9jGoxHEvq66Wo-wuKqouR3C). Carole Goble, 2020-03-25 ## Get involved diff --git a/project/acknowledgements.md b/project/acknowledgements.md index 21a7b0c..c3322f1 100644 --- a/project/acknowledgements.md +++ b/project/acknowledgements.md @@ -5,6 +5,7 @@ sidebar: false Main development, hosting and maintenance of WorkflowHub is done by the [eScience Lab](https://esciencelab.org.uk/) at The University of Manchester led by [Carole Goble](https://research.manchester.ac.uk/en/persons/carole.goble). + ## Funding @@ -25,12 +26,14 @@ We are also grateful for contributions by: * [BIOINDUSTRY 4.0](https://www.ibisba.eu/EU-Projects/Horizon-Europe) ([HORIZON-INFRA-2022-TECH-01 101094287](https://doi.org/10.3030/101094287), [UKRI 10048146](https://gtr.ukri.org/projects?ref=10048146)) * ..in addition to contributions from [WorkflowHub Club](#workflowhub-club) participants + ### EOSC-Life {% include affiliation-tiles-selection.html type="EOSC-Life"%} workflowhub.eu was founded as part of [**EOSC-Life**](https://www.eosc-life.eu/) ([WP2 _Tools Collaboratory_](https://github.com/eosc-life/tools-collaboratory-roadmap)), funded by European Union’s [Horizon 2020](https://ec.europa.eu/programmes/horizon2020/) programme under grant agreement [H2020-INFRAEOSC-2018-2 824087](https://doi.org/10.3030/824087). + ### Previous funding {% include affiliation-tiles-selection.html type="previous"%} @@ -49,6 +52,7 @@ Previous contributions were funded by: The main [WorkflowHub codebase](https://github.com/seek4science/seek/tree/workflowhub) is based on [SEEK](https://seek4science.org/about_us.html) and builds on previous experience with developing [myExperiment](https://www.myexperiment.org/about). SEEK is implemented in [Ruby on Rails](https://rubyonrails.org/) using a wide range of open source [Ruby gems](https://github.com/seek4science/seek/blob/workflowhub/Gemfile.lock). + ## Related projects ### ELIXIR @@ -66,6 +70,7 @@ WorkflowHub activities are strongly coordinated with [ELIXIR Europe](https://eli * [ELIXIR Netherlands](https://www.elixir-europe.org/about-us/who-we-are/nodes/netherlands) * [ELIXIR Hub](https://elixir-europe.org/about-us/who-we-are/hub) + ### Collaborations The WorkflowHub community collaborates closely with (at least) these projects: @@ -79,6 +84,7 @@ The WorkflowHub community collaborates closely with (at least) these projects: * [FAIRDOM](https://fair-dom.org) * [FAIRDOM-SEEK](https://fairdomseek.org/) + ## WorkflowHub Club The weekly [WorkflowHub Club](/project/community) is chaired by **Johan Gustafsson**. diff --git a/project/citation.md b/project/citation.md index 5dd34ec..d16d00d 100644 --- a/project/citation.md +++ b/project/citation.md @@ -1,5 +1,8 @@ --- title: Citation +sidebar: false --- {% include citation.md %} + +{% include callout.html type="tip" content="See also [publication and outreach](/project/outreach) for more specific work." %} diff --git a/project/outreach.md b/project/outreach.md index d6dcfbe..159d867 100644 --- a/project/outreach.md +++ b/project/outreach.md @@ -1,6 +1,7 @@ --- title: Outreach and Publications page_id: outreach +type: resource sidebar: false --- @@ -177,6 +178,7 @@ Gareth Price, Johan Gustafsson (2022): _Australian BioCommons Webinar_ + ### 2021 Carole Goble (2021): @@ -321,6 +323,11 @@ The Global Alliance for Genomics And Health (GA4GH) 10th Plenary Meeting. _F1000Research_ **11**:1318 (poster) +Carole Goble, Finn Bacall, Stian Soiland-Reyes, Stuart Owen, Alan Williams, Ignacio Eguinoa, Bert Droesbeke, Hervé Ménager, Laura Rodríguez Navas, José María Fernández, Salvador Capella-Gutierrez, Michael R. Crusoe, Björn Grüning, Simone Leo, Luca Pireddu, Johan Gustafsson, Phil Ewels, WorkflowHub Community, Frederik Coppens (2022): +[**WorkflowHub – a FAIR registry for workflows**](https://doi.org/10.7490/f1000research.1118984.1). +_ELIXIR All Hands 2022_, Amsterdam, Netherlands, 7-10 June 2022. + + Carole Goble, Finn Bacall, Stian Soiland-Reyes, Stuart Owen, Alan Williams, Ignacio Eguinoa, Bert Droesbeke, Hervé Ménager, Laura Rodriguez-Navas, José M. Fernández, Salvador Capella-Gutierrez, Michael R. Crusoe, Björn Grüning, Simone Leo, Luca Pireddu, Johan Gustafsson, Phil Ewels, WorkflowHub Community, Frederik Coppens (2021): [**The WorkflowHub: A FAIR Registry for Workflows and Workflow Research Objects**](https://drive.google.com/file/d/1Ge5bcKQBH03t5VH9IDIT0F8pfenNrw9-/view?usp=sharing). _[BOSC 2021](https://www.open-bio.org/events/bosc-2021/)_, diff --git a/project/roadmap.md b/project/roadmap.md index e50d705..87eca91 100644 --- a/project/roadmap.md +++ b/project/roadmap.md @@ -1,6 +1,7 @@ --- title: Roadmap page_id: roadmap +type: resource sidebar: false redirect_from: /roadmap/ --- From ef1f097070f0087c07f0b1df4209797abdf54b34 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 4 Nov 2024 12:16:44 +1030 Subject: [PATCH 18/31] Update tiles --- index.md | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/index.md b/index.md index 0b044f1..2c3bd47 100644 --- a/index.md +++ b/index.md @@ -46,19 +46,19 @@ For any kind of questions or suggestions on using WorkflowHub, feel free to join ## Project resources -{% include section-navigation-tiles-simple.html col = "3" type="resource"%} +{% include section-navigation-tiles-simple.html col = "2" type="resource"%} + +
+ Production instance + Sandbox instance (use for testing; occasionally wiped) + Source code + API documentation + GitHub issues +
* **Tutorial videos:** * [Make your workflows findable and citable](https://www.youtube.com/watch?v=2kGKxaPuQN8) ([slides](https://doi.org/10.5281/zenodo.7787488)) * [WorkflowHub ask-me-anything](https://workflowhub.eu/presentations/19?version=1) tutorial session -* **Production instance**: -* **Sandbox instance**: (use for testing; occasionally wiped) -* **Source code**: [seek4science/seek](https://github.com/seek4science/seek) -* **API documentation**: -* **EOSC-Life Deliverable 2.3**: -* **Tasks**: - * WorkflowHub implementation (SEEK) - * General WorkflowHub ## Get involved From cf0bdb8a454c0eb7f8e3bbe8bbaf3c1bc0a3b5ee Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 4 Nov 2024 12:22:13 +1030 Subject: [PATCH 19/31] Update tiles --- index.md | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/index.md b/index.md index 2c3bd47..af61b24 100644 --- a/index.md +++ b/index.md @@ -49,11 +49,9 @@ For any kind of questions or suggestions on using WorkflowHub, feel free to join {% include section-navigation-tiles-simple.html col = "2" type="resource"%}
- Production instance - Sandbox instance (use for testing; occasionally wiped) - Source code - API documentation - GitHub issues + Production instance + Sandbox instance (use for testing; occasionally wiped) + Source code
* **Tutorial videos:** From 05200190384817ba07cd71081136ebe69e0950fd Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 4 Nov 2024 12:26:20 +1030 Subject: [PATCH 20/31] Update tiles --- index.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/index.md b/index.md index af61b24..496a39b 100644 --- a/index.md +++ b/index.md @@ -48,10 +48,12 @@ For any kind of questions or suggestions on using WorkflowHub, feel free to join {% include section-navigation-tiles-simple.html col = "2" type="resource"%} -
- Production instance - Sandbox instance (use for testing; occasionally wiped) - Source code +
+
+ Production instance + Sandbox instance (use for testing; occasionally wiped) + Source code +
* **Tutorial videos:** From 178c9f1cae357c6db5e2465701b8248116cf4deb Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 4 Nov 2024 12:29:38 +1030 Subject: [PATCH 21/31] Update tiles --- index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.md b/index.md index 496a39b..30dba11 100644 --- a/index.md +++ b/index.md @@ -49,7 +49,7 @@ For any kind of questions or suggestions on using WorkflowHub, feel free to join {% include section-navigation-tiles-simple.html col = "2" type="resource"%}
-
+
Production instance Sandbox instance (use for testing; occasionally wiped) Source code From 85d64f312d029c5d44da005de2792452796ceb80 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 4 Nov 2024 12:51:54 +1030 Subject: [PATCH 22/31] Update tiles --- _data/tiles.yml | 2 ++ _includes/tiles-simple.html | 9 +++++++++ index.md | 4 ++-- 3 files changed, 13 insertions(+), 2 deletions(-) create mode 100644 _data/tiles.yml create mode 100644 _includes/tiles-simple.html diff --git a/_data/tiles.yml b/_data/tiles.yml new file mode 100644 index 0000000..055340f --- /dev/null +++ b/_data/tiles.yml @@ -0,0 +1,2 @@ +- title: "Production instance" + url: https://workflowhub.eu/ diff --git a/_includes/tiles-simple.html b/_includes/tiles-simple.html new file mode 100644 index 0000000..a5e4d5e --- /dev/null +++ b/_includes/tiles-simple.html @@ -0,0 +1,9 @@ +
+ {%- for item in site.data.tiles %} + {%- if item.title %} +
+ {{item.title}} +
+ {%- endif %} + {%- endfor %} +
\ No newline at end of file diff --git a/index.md b/index.md index 30dba11..14cfda2 100644 --- a/index.md +++ b/index.md @@ -46,11 +46,11 @@ For any kind of questions or suggestions on using WorkflowHub, feel free to join ## Project resources -{% include section-navigation-tiles-simple.html col = "2" type="resource"%} +{% include section-navigation-tiles-simple.html col = "2" type="resource" %} +{% include tiles-simple.html col = "2" %}
- Production instance Sandbox instance (use for testing; occasionally wiped) Source code
From bef1235e904187491ee3c7f59bd30d9c5e76b05c Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 4 Nov 2024 13:01:26 +1030 Subject: [PATCH 23/31] Update tiles --- _data/tiles.yml | 10 ++++++++++ _includes/tiles-simple.html | 2 +- index.md | 8 -------- 3 files changed, 11 insertions(+), 9 deletions(-) diff --git a/_data/tiles.yml b/_data/tiles.yml index 055340f..2e9319f 100644 --- a/_data/tiles.yml +++ b/_data/tiles.yml @@ -1,2 +1,12 @@ - title: "Production instance" url: https://workflowhub.eu/ +- title: "Sandbox instance (use for testing; occasionally wiped)" + url: https://dev.workflowhub.eu/ +- title: "Source code" + url: https://github.com/seek4science/seek +- title: "Documentation" + url: docs/ +- title: "Outreach and Publications" + url: project/outreach +- title: "Roadmap" + url: project/roadmap diff --git a/_includes/tiles-simple.html b/_includes/tiles-simple.html index a5e4d5e..0d3e50e 100644 --- a/_includes/tiles-simple.html +++ b/_includes/tiles-simple.html @@ -2,7 +2,7 @@ {%- for item in site.data.tiles %} {%- if item.title %}
- {{item.title}} + {{item.title}}
{%- endif %} {%- endfor %} diff --git a/index.md b/index.md index 14cfda2..7c33e15 100644 --- a/index.md +++ b/index.md @@ -46,16 +46,8 @@ For any kind of questions or suggestions on using WorkflowHub, feel free to join ## Project resources -{% include section-navigation-tiles-simple.html col = "2" type="resource" %} {% include tiles-simple.html col = "2" %} -
-
- Sandbox instance (use for testing; occasionally wiped) - Source code -
-
- * **Tutorial videos:** * [Make your workflows findable and citable](https://www.youtube.com/watch?v=2kGKxaPuQN8) ([slides](https://doi.org/10.5281/zenodo.7787488)) * [WorkflowHub ask-me-anything](https://workflowhub.eu/presentations/19?version=1) tutorial session From 7b759ec2ad368cf9306d6c5ddd6c5d8fda1ef9ba Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 4 Nov 2024 13:04:58 +1030 Subject: [PATCH 24/31] Update tiles --- _data/tiles.yml | 2 +- _includes/tiles-simple.html | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/_data/tiles.yml b/_data/tiles.yml index 2e9319f..a3fbbae 100644 --- a/_data/tiles.yml +++ b/_data/tiles.yml @@ -1,6 +1,6 @@ - title: "Production instance" url: https://workflowhub.eu/ -- title: "Sandbox instance (use for testing; occasionally wiped)" +- title: "Sandbox instance" url: https://dev.workflowhub.eu/ - title: "Source code" url: https://github.com/seek4science/seek diff --git a/_includes/tiles-simple.html b/_includes/tiles-simple.html index 0d3e50e..db642a3 100644 --- a/_includes/tiles-simple.html +++ b/_includes/tiles-simple.html @@ -2,7 +2,7 @@ {%- for item in site.data.tiles %} {%- if item.title %}
- {{item.title}} + {{item.title}}
{%- endif %} {%- endfor %} From 84221fe68d02ee927573a385a361ddc598e4ef13 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 4 Nov 2024 13:06:58 +1030 Subject: [PATCH 25/31] Update tiles --- _includes/tiles-simple.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_includes/tiles-simple.html b/_includes/tiles-simple.html index db642a3..5f7f25e 100644 --- a/_includes/tiles-simple.html +++ b/_includes/tiles-simple.html @@ -2,7 +2,7 @@ {%- for item in site.data.tiles %} {%- if item.title %}
- {{item.title}} + {{item.title}}
{%- endif %} {%- endfor %} From eeda416ea018fca964d7995d3273235fc4d945c9 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 4 Nov 2024 13:07:23 +1030 Subject: [PATCH 26/31] Update tiles --- _includes/tiles-simple.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_includes/tiles-simple.html b/_includes/tiles-simple.html index 5f7f25e..f9dafce 100644 --- a/_includes/tiles-simple.html +++ b/_includes/tiles-simple.html @@ -2,7 +2,7 @@ {%- for item in site.data.tiles %} {%- if item.title %}
- {{item.title}} + {{item.title}}
{%- endif %} {%- endfor %} From 2499b4fa29799f47b8a27826b002922b58b23e7d Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 4 Nov 2024 13:08:57 +1030 Subject: [PATCH 27/31] Update tiles --- _includes/tiles-simple.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_includes/tiles-simple.html b/_includes/tiles-simple.html index f9dafce..5f7f25e 100644 --- a/_includes/tiles-simple.html +++ b/_includes/tiles-simple.html @@ -2,7 +2,7 @@ {%- for item in site.data.tiles %} {%- if item.title %}
- {{item.title}} + {{item.title}}
{%- endif %} {%- endfor %} From 344d7c2f5f22824d0a1c0058d8e1b2e3da9b9058 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 4 Nov 2024 13:10:18 +1030 Subject: [PATCH 28/31] Update tiles --- _includes/tiles-simple.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_includes/tiles-simple.html b/_includes/tiles-simple.html index 5f7f25e..d666386 100644 --- a/_includes/tiles-simple.html +++ b/_includes/tiles-simple.html @@ -2,7 +2,7 @@ {%- for item in site.data.tiles %} {%- if item.title %}
- {{item.title}} + {{item.title}}
{%- endif %} {%- endfor %} From d756d5a3cf98a71b3ca9b5b12153d63b9a60d695 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 4 Nov 2024 13:18:37 +1030 Subject: [PATCH 29/31] Update index.md --- docs/index.md | 1 - index.md | 13 +++++++++---- project/outreach.md | 1 - project/roadmap.md | 1 - 4 files changed, 9 insertions(+), 7 deletions(-) diff --git a/docs/index.md b/docs/index.md index fc5a29e..9f26c4f 100644 --- a/docs/index.md +++ b/docs/index.md @@ -2,7 +2,6 @@ title: Documentation toc: false page_id: docs -type: resource redirect_from: - /docs/before-you-start/ - /docs/onboarding/ diff --git a/index.md b/index.md index 7c33e15..22e5644 100644 --- a/index.md +++ b/index.md @@ -13,10 +13,15 @@ sidebar: true This website describes the open source **project** for developing and running [WorkflowHub](https://workflowhub.eu/). -* [WorkflowHub](https://workflowhub.eu) is a domain-agnostic workflow registry designed around [FAIR principles](https://workflows.community/groups/fair/). -* WorkflowHub is *workflow management system agnostic*: workflows may remain in their native repositories in their native forms. -* WorkflowHub provides features such as community spaces, collections, versioning and snapshots, and contributor credit. -* WorkflowHub allows workflows to be FAIR, citable, have managed *metadata* profiles, and be openly available for review and analytics. +[WorkflowHub](https://workflowhub.eu): + +* Is a domain-agnostic workflow registry designed around [FAIR principles](https://workflows.community/groups/fair/). +* Is *workflow management system agnostic*: workflows may remain in their native repositories in their native forms. +* Provides features such as community spaces, collections, versioning and snapshots, and contributor credit. +* Allows workflows to be FAIR, citable, have managed *metadata* profiles, and be openly available for review and analytics. + +In addition: + * Workflows are packaged, registered, downloaded and exchanged as [workflow-centric Research Objects](/Workflow-RO-Crate/) using the [RO-Crate](https://w3id.org/ro/crate) specification, with test and example data, managed metadata profiles, citations and more. * A [schema.org](https://schema.org/) based Bioschemas profile describes the metadata about a workflow and use of the [Common Workflow Language](https://www.commonwl.org/) is encouraged, providing a canonical description of the workflow itself. * Popular workflow management systems such as [Galaxy](https://galaxyproject.org/), [Nextflow](https://nextflow.io/), and [Snakemake](https://snakemake.readthedocs.io/) are working with the Hub to seamlessly and automatically support object packaging, registration and exchange. diff --git a/project/outreach.md b/project/outreach.md index 159d867..c95cd36 100644 --- a/project/outreach.md +++ b/project/outreach.md @@ -1,7 +1,6 @@ --- title: Outreach and Publications page_id: outreach -type: resource sidebar: false --- diff --git a/project/roadmap.md b/project/roadmap.md index 87eca91..e50d705 100644 --- a/project/roadmap.md +++ b/project/roadmap.md @@ -1,7 +1,6 @@ --- title: Roadmap page_id: roadmap -type: resource sidebar: false redirect_from: /roadmap/ --- From c445ab87bf5688ce63c4b7528193b9c074b4df9b Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 4 Nov 2024 17:30:47 +1030 Subject: [PATCH 30/31] Update index.md and roadmap.md --- index.md | 20 ++++++-------------- project/roadmap.md | 10 ++++------ 2 files changed, 10 insertions(+), 20 deletions(-) diff --git a/index.md b/index.md index 22e5644..5dfada0 100644 --- a/index.md +++ b/index.md @@ -9,16 +9,14 @@ sidebar: true ## About -[WorkflowHub](https://workflowhub.eu/) is a FAIR registry for describing, sharing and publishing scientific computational workflows. The registry is sponsored by the European RI Cluster EOSC-Life, the European Research Infrastructure ELIXIR, and [multiple EU-wide projects](/project/acknowledgements/#funding). - -This website describes the open source **project** for developing and running [WorkflowHub](https://workflowhub.eu/). +This website describes the open source project for developing and running [**WorkflowHub**](https://workflowhub.eu/): a FAIR registry for describing, sharing and publishing scientific computational workflows. The registry is sponsored by the European RI Cluster EOSC-Life, the European Research Infrastructure ELIXIR, and [multiple EU-wide projects](/project/acknowledgements/#funding). [WorkflowHub](https://workflowhub.eu): -* Is a domain-agnostic workflow registry designed around [FAIR principles](https://workflows.community/groups/fair/). -* Is *workflow management system agnostic*: workflows may remain in their native repositories in their native forms. +* Is a **domain-agnostic** workflow registry designed around [FAIR principles](https://workflows.community/groups/fair/). +* Is **workflow management system agnostic**: workflows may remain in their native repositories in their native forms. * Provides features such as community spaces, collections, versioning and snapshots, and contributor credit. -* Allows workflows to be FAIR, citable, have managed *metadata* profiles, and be openly available for review and analytics. +* Allows workflows to be FAIR, citable, have managed metadata profiles, and be openly available for review and analytics. In addition: @@ -81,16 +79,10 @@ For asynchronous communication, see also: ### Development -Created as part of the [EOSC-Life](https://www.eosc-life.eu) WP2 [Tools Collaboratory](https://github.com/eosc-life/tools-collaboratory-roadmap), WorkflowHub is in production but still under active development. - -See a complete list of contributors on the [acknowledgement](/project/acknowledgements) page. +Created as part of the [EOSC-Life](https://www.eosc-life.eu) WP2 [Tools Collaboratory](https://github.com/eosc-life/tools-collaboratory-roadmap), WorkflowHub is in production but still under active development. See the [roadmap page](/project/roadmap) for a list of in-flight and future development activities. -Aims of the project include: +You can also see a complete list of contributors on the [acknowledgements](/project/acknowledgements) page. -* Evolvement of [myExperiment](https://myexperiment.org/) that is workflow system agnostic, supports a repository of workflows in native and standardised form (e.g. [CWL](https://www.commonwl.org/) and the virtual aggregation of established tool, workflow and registries to support discovery over a fragmented ecosystem. The federated registry would support a **common API** to simplify access for tool developers. -* Standardised workflow identifiers and metadata descriptions needed for workflow discovery, reuse, preservation, interoperability and monitoring and metadata harvesting using standard protocols. Workflows are usually multi-component (requiring links to test data, example runs, explanatory documentation, etc) and used in collections for scientific use cases. We plan to use the Research Object specification for packaging workflows, which has already been combined with [CWL](https://www.commonwl.org/) and is part of the [BioComputeObject](http://biocomputeobject.org/) specification. -* Workflow snapshot preservation, publishing, citation and monitoring, credit claiming and workflows part of the scholarly communication landscape partnering with platforms like [DataCite](https://datacite.org/) and EOSC’s [OpenAIRE](https://www.openaire.eu/) and their Research Community Dashboards linking publications with workflows, associated datasets, software, etc. -* The workflow registry is planned to be based on the [SEEK platform](https://seek4science.org/) using [Common Workflow Language](https://www.commonwl.org/) and [Research Objects](http://www.researchobject.org/) to glue in federated workflow and tool descriptions across the research infrastructures. ### Contact Us diff --git a/project/roadmap.md b/project/roadmap.md index e50d705..3e58d3a 100644 --- a/project/roadmap.md +++ b/project/roadmap.md @@ -6,15 +6,13 @@ redirect_from: /roadmap/ --- -_Please feel free to help contribute to this roadmap through the [WorkflowHub Club](/community/) or as [feedback](https://workflowhub.eu/home/feedback)!_ +{% include callout.html type="note" content="_Please feel free to help contribute to this roadmap through the [WorkflowHub Club](/community/) or as [feedback](https://workflowhub.eu/home/feedback)!_" %} -Please note that the roadmap isn't a project plan or release schedule. + +Please note that the roadmap is not a project plan or release schedule. The WorkflowHub Club is a very dynamic and agile team, and the roadmap is reviewed and updated regularly. -It's purpose is to give a general indication of intent and direction of travel. +Its purpose is to give a general indication of intent and direction of travel. -See also: - * WorkflowHub implementation (SEEK) - * General WorkflowHub