diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml index 3bb0518..cdc8cea 100644 --- a/.github/workflows/jekyll.yml +++ b/.github/workflows/jekyll.yml @@ -17,7 +17,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: ref: ${{ github.event.inputs.branch }} @@ -30,7 +30,7 @@ jobs: - name: Setup Pages id: pages - uses: actions/configure-pages@v2 + uses: actions/configure-pages@v5 - name: Install dependencies run: | @@ -46,4 +46,4 @@ jobs: JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - name: Upload artifact - uses: actions/upload-pages-artifact@v1 + uses: actions/upload-pages-artifact@v3 diff --git a/_config.yml b/_config.yml index 2fe8cfa..f751574 100644 --- a/_config.yml +++ b/_config.yml @@ -4,7 +4,7 @@ description: > Project pages for developing and running WorkflowHub, a registry of scientific workflows. -remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@2.5.0 +remote_theme: ELIXIR-Belgium/elixir-toolkit-theme permalink: pretty diff --git a/_data/glossary.yml b/_data/glossary.yml new file mode 100644 index 0000000..5af6b12 --- /dev/null +++ b/_data/glossary.yml @@ -0,0 +1,25 @@ +- title: "Team" + description: Project, also called “Team” + url: +- title: "Workflow type" + description: See supported workflow types +- title: "Organisation" + description: + url: +- title: "Space" + description: + url: +- title: "Main workflow file" + description: This is the main workflow file that has to be uploaded/referenced. Specify the Workflow type of the main workflow in the dropdown list (i.e. Common Workflow Language ".cwl", Galaxy ".ga", KNIME ".knwf", Nextflow ".nf", Snakemake ".snake". If your workflow type is not listed, please choose "other". +- title: "Git repository" + description: + url: +- title: "Remote file URL" + description: +- title: "CWL abstract" + description: The CWL abstract is used as a summary of the workflow to parse for example the description (doc) if provided or to generate a svg diagram. If you have a Galaxy workflow you can generate the CWL abstract with galaxy2cwl. If your main workflow is a CWL workflow, you can skip this step. In the future it will also be possible to convert other workflow types to CWL abstract. +- title: "Diagram" + description: If your main workflow file is CWL or you give a CWL abstract, the diagram is automatically generated by the WorkflowHub website. In any other case, you will have to supply a diagram yourself, which will then be included in the workflow entry on WorkflowHub (and by extension in the RO-Crate). During registration, you can use the upload / reference fields to attach a diagram in .svg (preferred) or .jpeg/.png format. +- title: "RO-Crate" + description: Research Object Crate (RO-crate) + url: https://www.researchobject.org/ro-crate/ diff --git a/_data/resources.yml b/_data/resources.yml new file mode 100644 index 0000000..7c918f4 --- /dev/null +++ b/_data/resources.yml @@ -0,0 +1,15 @@ +- title: "Common Workflow Language (.cwl)" + url: https://www.commonwl.org/ + url_community_workflows: https://github.com/common-workflow-library + url_community: https://www.commonwl.org/community/ +- title: "Nextflow (.nf)" + url: https://www.nextflow.io/ + url_community_workflows: https://nf-co.re/pipelines/ + url_community: https://nf-co.re/ +- title: "SnakeMake (.snake)" + url: https://snakemake.github.io/ + url_community_workflows: https://snakemake.github.io/snakemake-workflow-catalog/ +- title: "KNIME (.knwf)" + url: https://www.knime.com/ + url_community_workflows: https://hub.knime.com/ + diff --git a/_data/sidebars/documentation.yml b/_data/sidebars/documentation.yml index 6d4fa95..5a3d382 100644 --- a/_data/sidebars/documentation.yml +++ b/_data/sidebars/documentation.yml @@ -1,49 +1,44 @@ title: Documentation subitems: - - title: Quick start guide + - title: Getting started url: /docs/index - title: Complete guide to using WorkflowHub url: /docs/guide-to-using-workflowhub - - title: Detailed documentation + - title: Finding workflows + url: /docs/finding-workflows/ + - title: Test submissions to WorkflowHub + url: /docs/workflowhub_instances/ + - title: Getting set up on WorkflowHub + url: /docs/organising-and-setup/ + subitems: + - title: How to register with WorkflowHub + url: /docs/how-to-register/ + - title: Logging in + url: /docs/logging-in/ + - title: Join or set up Teams & Spaces + url: /docs/join-create-teams-spaces/ + - title: What are Teams, Spaces and Organizations? + url: /docs/space-team-organisation/ + - title: Contributing workflows + url: /docs/registering_workflows/registering-a-workflow/ subitems: - - title: WorkflowHub instances - url: /docs/workflowhub_instances/ - - title: How to register - url: /docs/how-to-register/ - - title: Logging in - url: /docs/logging-in/ - - title: What are Teams, Spaces and Organizations? - url: /docs/space-team-organisation/ - - title: Join or set up Teams & Spaces - url: /docs/join-create-teams-spaces/ - - title: Registering workflows - url: /docs/registering_workflows/registering-a-workflow/ - subitems: - title: Register and login url: /docs/registering_workflows/register-and-login/ - title: Adding files url: /docs/registering_workflows/adding-files/ - title: Complete workflow metadata url: /docs/registering_workflows/complete-workflow-metadata/ - - title: Check uploaded workflow + - title: Finalise registration url: /docs/registering_workflows/check-uploaded-workflow/ - title: Supported workflow types url: /docs/registering_workflows/supported-workflow-types/ - - title: Organising your workflows on WorkflowHub - url: /docs/organising-workflows/ - - title: Maintaining your workflow - url: /docs/maintaining-your-workflow/ - - title: Mint a DOI for your workflow - url: /docs/citable/ - - title: Finding workflows - url: /docs/finding-workflows/ - - title: Metadata list - url: /docs/metadata-list/ - - title: Glossary - url: /docs/glossary/ - - title: For developers - url: /developer/ - subitems: + - title: Maintain your workflows + url: /docs/maintaining-your-workflow/ + - title: Mint a workflow DOI + url: /docs/citable/ + - title: For developers + url: /developer/ + subitems: - title: Bioschemas.org url: /developer/bioschemas/ - title: Workflow RO-Crate @@ -52,5 +47,11 @@ subitems: url: /developer/how-to-make-a-workflow-ro-crate/ - title: RO-Crate API url: /developer/ro-crate-api/ - - title: TRS + - title: TRS API url: /developer/trs/ + - title: FAQ + url: /docs/faq/ + - title: Metadata list + url: /docs/metadata-list/ + - title: Glossary + url: /docs/glossary/ diff --git a/_includes/glossary.html b/_includes/glossary.html new file mode 100644 index 0000000..88cd439 --- /dev/null +++ b/_includes/glossary.html @@ -0,0 +1,34 @@ +{%- if include.tag %} +{%- assign tools = site.data.glossary | add_related_pages | where:"related_pages", include.tag | sort_natural: "name" %} +{%- else %} +{%- assign tools = site.data.glossary | add_related_pages | sort_natural: "name" %} +{%- endif %} +{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %} +{%- unless tools.size == 0 or tools == nil %} +Skip tool table +
+ + + + + + + + + {%- for tool in tools %} + + {% if tool.url %} + + {%- else %} + + {%- endif %} + {% if tool.description %} + + {%- endif %} + + {%- endfor %} + +
TermDescription
{{tool.title}}{{tool.title}}{{tool.description}}
+
+{%- endunless %} +
\ No newline at end of file diff --git a/_includes/resources.html b/_includes/resources.html new file mode 100644 index 0000000..40c8072 --- /dev/null +++ b/_includes/resources.html @@ -0,0 +1,43 @@ +{%- if include.tag %} +{%- assign tools = site.data.resources | add_related_pages | where:"related_pages", include.tag | sort_natural: "name" %} +{%- else %} +{%- assign tools = site.data.resources | add_related_pages | sort_natural: "name" %} +{%- endif %} +{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %} +{%- unless tools.size == 0 or tools == nil %} +Skip tool table +
+ + + + + + + + + {%- for tool in tools %} + + {% if tool.url %} + + {%- else %} + + {%- endif %} + + + {%- endfor %} + +
WfMSLinks to related information {%- if include.tag -%} + + + {%- endif %} +
{{tool.title}}{{tool.title}} + {%- if tool.url_community %} + Community + {%- endif %} + {%- if tool.url_community_workflows %} + Community workflows + {%- endif %} +
+
+{%- endunless %} +
\ No newline at end of file diff --git a/_sass/_custom_classes.scss b/_sass/_custom_classes.scss index b661935..d765252 100644 --- a/_sass/_custom_classes.scss +++ b/_sass/_custom_classes.scss @@ -1,3 +1,24 @@ +/*-----Navigation tiles-----*/ +/*-----From https://github.com/elixir-europe/infectious-diseases-toolkit/blob/main/_sass/_custom_classes.scss-----*/ + +.navigation-tiles { + .card { + background-color: $light; + color: $dark; + } + .card:hover { + box-shadow: $box-shadow; + background-color: $primary; + } + + .card-body { + h3 { + color: $dark; + font-size: 1.2rem; + } + } +} + /*-----Top navigation-----*/ header .navbar { .navbar-brand { diff --git a/_sass/_custom_variables.scss b/_sass/_custom_variables.scss index e69e641..17b7ad1 100644 --- a/_sass/_custom_variables.scss +++ b/_sass/_custom_variables.scss @@ -3,3 +3,8 @@ $topnav-bg: $light; $topnav-title-color: $primary; $topnav-brand-height: 80px; +/*-----Section navigation tiles-----*/ +$nav-card-bg: $primary; +$nav-card-color: $dark; +$nav-card-bg-hover: $primary; +$nav-card-color-hover: $white; diff --git a/developer/how-to-make-a-workflow-ro-crate.md b/developer/how-to-make-a-workflow-ro-crate.md index 7722897..bf039c5 100644 --- a/developer/how-to-make-a-workflow-ro-crate.md +++ b/developer/how-to-make-a-workflow-ro-crate.md @@ -1,16 +1,17 @@ --- -title: How to make a workflow RO-crate? +title: How to make a workflow RO-crate redirect_from: /how-to-make-a-workflow-ro-crate/ --- More info about workflow RO-crate specification can be found in our [Workflow-RO-Crate](/Workflow-RO-Crate/) section. -### 1. Using the WorkflowHub website +## 1. Using the WorkflowHub website -The most convenient way to make a workflow RO-crate at this moment is by making use of WorkflowHub capabilities. The website is able to generate RO-crates based on an uploaded/referenced workflow file and some general metadata that is requested through a form. After the workflow is [registered](/docs/registering-a-workflow) for more info about this topic) it is possible to download the RO-crate with the download button. The generated RO-crate, basically a zip file, will contain these elements: +The most convenient way to make a workflow RO-crate at this moment is by making use of WorkflowHub capabilities. The website is able to generate RO-crates based on an uploaded/referenced workflow file and some general metadata that is requested through a form. After the workflow is [registered](/docs/registering-a-workflow) for more info about this topic) it is possible to download the RO-crate with the download button. -- **JSONLD file**\ - JSONLD serving machine readable metadata including: +The generated RO-crate, basically a zip file, will contain these elements: + +- **JSONLD file**: JSONLD serving machine-readable metadata including: - Author - Contents and structure - Project @@ -24,23 +25,19 @@ The most convenient way to make a workflow RO-crate at this moment is by making The metadata properties are based on the [BioSchemas workflow profile](https://bioschemas.org/profiles/Workflow) . -- **HTML file**\ - A web page serving the metadata in a human readable way. +- **HTML file**: A web page serving the metadata in a human-readable way. - Original URL - Author (creators) - License - Contents -- **Main Workflow file**\ - The workflow file itself if uploaded. +- **Main Workflow file**: The workflow file itself, if uploaded. -- **Main Workflow Diagram (optional)**\ - A diagram visualizing the steps in the workflow if uploaded or generated out of the CWL. +- **Main Workflow Diagram (optional)**: A diagram visualizing the steps in the workflow, if uploaded or generated from CWL. -- **Main Workflow CWL Description (optional)**\ - This file can be included if supplied by the user. +- **Main Workflow CWL Description (optional)**: This file can be included if supplied by the user. -### 2. Making one offline yourself +## 2. Making one offline yourself We are working on a python package at this moment to wrap your own RO-crates. This will allow you to not be bounded by the file limitations of the WorkflowHub website (workflow + CWL abstract and/or diagram), and will make it possible to automate the RO-Crate generation. The python package can be found in [ResearchObject/ro-crate-py](https://github.com/ResearchObject/ro-crate-py). diff --git a/developer/index.md b/developer/index.md index f0ca05b..ab6132b 100644 --- a/developer/index.md +++ b/developer/index.md @@ -1,5 +1,8 @@ --- -title: For developers +title: Documentation for developers +description: Documentation for developers, including bioschemas, RO-crate, and APIs. +page_id: developer +toc: false --- Programmatic access to WorkflowHub is based on [FAIRDOM-SEEK](https://seek4science.org/) and [RO-Crate](https://www.researchobject.org/ro-crate/): @@ -9,3 +12,14 @@ Programmatic access to WorkflowHub is based on [FAIRDOM-SEEK](https://seek4scien * [Workflow RO-Crate](../Workflow-RO-Crate) including [How to make Workflow RO-Crate](how-to-make-a-workflow-ro-crate/) and [RO-Crate API](ro-crate-api/) * [FAIR Signposting](signposting/) and FAIR Digital Objects (FDO) * [GA4GH’s Tool Registry Service API](trs/) for iterating over every workflow + + +### Reference material + +WorkflowHub is based on the [SEEK framework](https://docs.seek4science.org/). Below is a map between WorkflowHub terms and the underlying SEEK definitions and documentation. + +|WorkflowHub term|FAIRDOM SEEK term|Explanation|Link| +|-----|-----|-----|-----| +|Team|Project|Set up for a specific activity or group|| +|Space|Programme|Set up for a funded piece of work, project or consortium|| + diff --git a/docs/citable.md b/docs/citable.md index c6d77bd..2bd4918 100644 --- a/docs/citable.md +++ b/docs/citable.md @@ -1,65 +1,75 @@ --- -title: Citable workflows +title: Creating a citable workflow +page_id: citable +description: How to mint a digital object identifier (DOI) and create a citation for your workflow. redirect_from: /citable/ --- -Workflows registered in that are _public_ can be assigned a [DOI](https://www.doi.org/) (Digital Object Identifier) so that they can more easily be cited in academic work. +Workflows registered in that are _public_ can be assigned a [DOI](https://www.doi.org/) (Digital Object Identifier) so that they can more easily be cited in academic work. WorkflowHub DOIs are registered with [DataCite](https://datacite.org/) using the [DataCite Metadata Schema](https://schema.datacite.org/), meaning that the metadata joins the scholarly knowledge graphs [DataCite Commons PID Graph](https://commons.datacite.org/doi.org?query=client.uid:borq.00002-2021) and [OpenAIRE Research Graph](https://graph.openaire.eu/) ([example](https://explore.openaire.eu/search/software?pid=10.48546%2Fworkflowhub.workflow.160.1)). -WorkflowHub DOIs are registered with [DataCite](https://datacite.org/) using the [DataCite Metadata Schema](https://schema.datacite.org/), meaning that the metadata joins the scholarly knowledge graphs [DataCite Commons PID Graph](https://commons.datacite.org/doi.org?query=client.uid:borq.00002-2021) and [OpenAIRE Research Graph](https://graph.openaire.eu/) ([example](https://explore.openaire.eu/search/software?pid=10.48546%2Fworkflowhub.workflow.160.1)). +- You can assign DOIs for workflows you have registered and that you have been given write access to. +- You are not able to make DOIs for other people's workflows. +- Each version of the workflow must be registered separately. +- You can create a [new version](/docs/maintaining-your-workflow) of a workflow that has been assigned a DOI, without needing to assign a DOI to the new version. -## Assign a workflow DOI +{% include callout.html type="note" content="DOI minting is only enabled on the production instance (https://workflowhub.eu/), although you can try the below instructions up to the Publish step on the sandbox instance (https://dev.workflowhub.eu/)." %} -You can assign DOIs for workflows you have registered and that you have been given write access to. You are not able to make DOIs for other people's workflows. -Each version of the workflow must be registered separately. You can create a [new version](https://about.workflowhub.eu/Updating-a-registered-workflow/) of a workflow that has been assigned a DOI, without necessarily giving the new version a DOI yet. +## Creating a DOI -Note that DOI minting is only enable on the production instance , although you can try the below instructions up to the _"Publish"_ step on the sandbox instance . +### 1. Check metadata -### Check metadata +Before you mint a DOI, make sure you check the correctness of the [metadata for the workflow entry](/docs/registering_workflows/check-uploaded-workflow), and that it makes sense globally, as this will be part of the DataCite registration. -Before you mint a DOI, make sure you check the correctness of the [metadata of the workflow entry](https://about.workflowhub.eu/Registering-a-workflow-with-a-diagram-and-abstract-CWL/), and that it makes sense globally, as this will be part of the DataCite registration. Use _Actions -> Edit Workflow_ and _Actions -> Manage workflow_ to fill in: +Use `Actions` -> `Edit Workflow` and `Actions` -> `Manage workflow` to fill in: + * Title (is it specific enough) + * Creators (you can include registered WorkflowHub users or others by name) + * Status of workflow + * Description + * License -* Title (is it specific enough) -* Creators (you can include registered WorkflowHub users or others by name) -* Status of workflow -* Description -* License +{% include callout.html type="tip" content="For each of the registered users, it may be good to check that their [ORCID](https://orcid.org/) identifier has been registered. This ensures that the people will be uniquely identified. Users can edit My Profile to link to ORCID." %} -For each of the registered users, it may be good to check that their [ORCID](https://orcid.org/) identifier has been registered. This ensures that the people will be uniquely identified. Users can edit _"My Profile"_ to link to ORCID. -### Freezing the Workflow version +### 2. Freeze the workflow version -Before we can mint a DOI, we need to _freeze_ the version of the workflow in WorkflowHub, so that its metadata stay consistent with the DOI registration. +Before we can mint a DOI, we need to _freeze_ the version of the workflow in WorkflowHub, so that its metadata stays consistent with the metadata used for the DOI registration with DataCite. + +The next step towards a workflow DOI is shown in the `Citation` panel that appears on the right hand side of your workflow entry. In the image below, you can see that the next step is to _Freeze_ the workflow version. ![Freeze version](https://user-images.githubusercontent.com/253413/151150858-53c72ec7-3b9d-4349-9b99-8449eea396f9.png) -### Publishing workflow + +### 3. Publish the workflow + +If your workflow is not public, the next step is to publish the workflow so that it is _Public_. You can do this by clicking the `Publish `button in the `Citation` panel (see below). ![public](https://user-images.githubusercontent.com/253413/151160453-e471389f-1824-4390-a182-59ee8d684d4d.png) -You need to check this workflow is _Public_. Either click the button as above, or edit under _Manage Workflow_: + You can also check, and edit, sharing permissions by selecting `Manage Workflow` in the `Actions` drop down menu. ![permissions](https://user-images.githubusercontent.com/253413/151153355-2eefc5e6-c019-43bd-b041-633c7e15fb4c.png) -### Generate DOI +### 4. Generate a DOI -Now we can create a DOI: +Now you can use the `Citation` panel to create a DOI. ![Generate a DOI](https://user-images.githubusercontent.com/253413/151153468-b6e63f0f-955c-4d08-aeec-9183a00ee840.png) -A pop-up will remind you to revise the metadata and confirm: +A pop-up will remind you to revise the metadata and confirm. ![Comfirm DOI](https://user-images.githubusercontent.com/253413/151153585-994b0d33-74c9-4ab3-b1b5-7a8669405810.png) -### Finding DOI +## Finding DOIs DOIs that have been minted for workflows are shown as part of the workflow entry: ![doi in listing](https://user-images.githubusercontent.com/253413/151153977-ece6cfe0-4aa1-437b-a7f8-7e0a395d76f9.png) -### Citing Workflows + +## Citing Workflows You can generate a citation for a chosen journal style in the _Citation_ box: @@ -70,18 +80,16 @@ Note that as this generated citation is based on the corresponding [CSL styles]( Therefore remember to add the DOI to the citation in your reference manager, for instance as a comment or URL. Example: - -Douglas Lowe and Genís Bayarri. 2021. “Protein Ligand Complex MD Setup Tutorial Using BioExcel Building Blocks (Biobb) (Jupyter Notebook).” _WorkflowHub_. - +> Douglas Lowe and Genís Bayarri. 2021. “Protein Ligand Complex MD Setup Tutorial Using BioExcel Building Blocks (Biobb) (Jupyter Notebook).” _WorkflowHub_. -### Retrieving DataCite metadata +## Retrieving DataCite metadata You can look up the DataCite metadata of WorkflowHub DOI registrations using their [programmatic APIs](https://datacite.org/integratorapis.html) or the [DataCite Commons](https://commons.datacite.org/). For instance, from we can download the metadata as [DataCite XML](https://api.datacite.org/application/vnd.datacite.datacite+xml/10.48546/workflowhub.workflow.56.2), [DataCite JSON](https://api.datacite.org/application/vnd.datacite.datacite+json/10.48546/workflowhub.workflow.56.2), [Schema.org JSON-LD](https://api.datacite.org/application/vnd.schemaorg.ld+json/10.48546/workflowhub.workflow.56.2), [CiteProc JSON](https://api.datacite.org/application/vnd.citationstyles.csl+json/10.48546/workflowhub.workflow.56.2), [BibTex](https://api.datacite.org/application/x-bibtex/10.48546/workflowhub.workflow.56.2), [RIS](https://api.datacite.org/application/x-research-info-systems/10.48546/workflowhub.workflow.56.2). -**Note**: The schema.org metadata rendered by DataCite may differ slightly from the more complete metadata embedded in a WorkflowHub entry's HTML and RO-Crate. +{% include callout.html type="note" content="The schema.org metadata rendered by DataCite may differ slightly from the more complete metadata embedded in a WorkflowHub entry's HTML and RO-Crate." %} Example of returned DataCite XML following [DataCite Schema 4.3](https://schema.datacite.org/meta/kernel-4.3/): @@ -113,13 +121,13 @@ This tutorial aims to illustrate the process of setting up a simulation system c ``` -**Tip**: You can access these citations programmatically using DataCite's [content negotiation](https://support.datacite.org/docs/datacite-content-resolver) on resolving the DOI. +{% include callout.html type="tip" content="You can access these citations programmatically using DataCite's [content negotiation](https://support.datacite.org/docs/datacite-content-resolver) on resolving the DOI." %} -### Citing a Workflow without a DOI -Note that if a workflow has not got a DOI, you can still cite it using the versioned WorkflowHub _SEEK ID_, e.g. +## Citing a workflow without a DOI -You will need to generate the metadata (e.g. _title_ yourself as it has not been verified for citation by the authors. +Note that if a workflow does not have a DOI, you can still cite it using the versioned WorkflowHub _SEEK ID_, e.g. -Warning: As workflow versions without DOIs may not be frozen, it is also possible that the author later decides to withdraw the workflow from public view. Authors may subsequently edit the metadata of a given version, but not its downloadable content. +You will need to generate the metadata (e.g. _title_) yourself as it has not been verified for citation by the authors. +{% include callout.html type="warning" content="As workflow versions without DOIs may not be frozen, it is also possible that the author later decides to withdraw the workflow from public view. Authors may subsequently edit the metadata of a given version, but not its downloadable content." %} diff --git a/docs/finding-workflows.md b/docs/finding-workflows.md index c86e6df..9656678 100644 --- a/docs/finding-workflows.md +++ b/docs/finding-workflows.md @@ -1,35 +1,32 @@ --- -title: How to find and retrieve workflow(s) from WorkflowHub? +title: Find and retrieve workflows +description: How to find and retrieve workflows using WorkflowHub. +page_id: finding redirect_from: /How-to-find-and-retrieve-workflow(s)-from-WorkflowHub/ --- -### How to search for workflows +## How to search for workflows + You can find and retrieve any workflow from WorkflowHub by: -* Clicking on the “**Discover**” icon in the main page -or -* Clicking “**Browse**” in the navigation menu bar and then select “Workflow” +1. Clicking on the `Discover` icon on the [WorkflowHub main page](https://workflowhub.eu/), or +2. Clicking `Browse` in the top navigation bar and then selecting `Workflow`, or +3. Using the Search bar at the top of the main page -or -* Using the Search bar on the top of the page +If you want to find and retrieve only your own workflows, you have to: -If you want to find and retrieve only your own workflow, you have to: -* Log in -* Click on the dropdown list next to your name, in the upper right corner of the page -* Select “**My items**” or “**My projects**” -* Click on the “**Workflow**” button that will be shown in the page +1. Log in +2. Click on the dropdown list next to your name, in the upper right corner of the page +3. Select `My items` or `My projects` +4. Click on the `Workflow` button that is shown on the page -Workflows can be -* Viewed -* Downloaded -* Edited +Workflows can be viewed, downloaded, and / or edited depending on their associated sharing permissions. -according to the associated sharing permission. +## Filtering and sorting workflows -### Filtering and sorting workflows You can refine and filter the result of your search by using the filter sidebar on the left. -You can sort the result of your search by choosing a sorting criteria from the dropdown list shown in the upper right corner of your result page. +You can also sort the result of your search by choosing a sorting criteria from the dropdown list shown in the upper right corner of your result page. diff --git a/docs/glossary.md b/docs/glossary.md index 005af88..4cbd923 100644 --- a/docs/glossary.md +++ b/docs/glossary.md @@ -1,211 +1,8 @@ --- title: Glossary +description: A list of key terms used by the WorkflowHub registry. +page_id: glossary +toc: false --- -## General - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Project also called “Team” - -
Workflow type - - See supported workflow types -
Organisation - -
Space - -
Main workflow file -

- (mandatory)

- 		This is the main workflow file that has to be uploaded/referenced. -

- Specify the Workflow type of the main workflow in the dropdown list:

-
    - -
  • Common Workflow Language(.cwl),
    • - -
  • Galaxy(.ga),
    • - -
  • KNIME(.knwf),
    • - -
  • Nextflow(.nf) or
    • - -
  • Snakemake(.snake).
    • - -
  • If your workflow type is not listed, please choose other
    • -
-
Git repository - -
Remote file URL - -
CWL abstract -
(optional) - 		The CWL abstract is used as a summary of the workflow to parse for example the description (doc) if provided or to generate a svg diagram. If you have a Galaxy workflow you can generate the CWL abstract with galaxy2cwl. If your main workflow is a CWL workflow, you can skip this step. In the future it will also be possible to convert other workflow types to CWL abstract. -
Diagram -
(optional) - 		If your main workflow file is CWL or you give a CWL abstract, the diagram is automatically generated by the WorkflowHub website. In any other case you want a diagram in the RO-Crate and on the WorkflowHub website, you will have to supply one yourself. In the upload/reference fields you can attach your diagram in .svg (preferred) or .jpeg/.png. -
RO-Crate - Research Object Crate: https://www.researchobject.org/ro-crate/ -
- - - -## Extra Galaxy information {#galaxy} - - - - - - - - - - - - - - - - - - - - - - - -
How to use Galaxy - Information on how to use galaxy can be found on the Galaxy Training Network. -
Extract a workflow from the History - This is the most easy way to generate a Galaxy workflow and is extensively explained here. -
Editing a Galaxy workflow - Using the Galaxy workflow editor it is recommended to add tags and/or add for example the tutorial title as Annotation/Notes. More information on how to use the editor can be found here in the "The workflow editor" section. -
Galaxy to CWL abstract - Galaxy workflows can easily be converted to CWL abstract with galaxy2cwl. This can be seen as a standardized summary of the workflow that can be interpreted by WorkflowHub. CWL abstract can also be used to generate a diagram. -
Uploading to WorkflowHub - Since it is not possible to reference a workflow in a Galaxy instance, you either have to download the workflow file and upload it to WorkflowHub, or make an RO-Crate following the steps below. You can still reference the workflow in the galaxy instance using the source property in the metadata of the registration. -
- - - -## Extra Common Workflow Language (.cwl) information {#cwl} - - - - - - - - - - - -
Home page - https://www.commonwl.org/ -
Community workflows page - https://github.com/common-workflow-library -
- - - - -## Extra Nextflow (.nf) information {#nextflow} - - - - - - - - - - - -
Home page - https://www.nextflow.io/ -
Community workflows page - https://nf-co.re/ -
- - - -## Extra SnakeMake (.snake) information {#snakemake} - - - - - - - - - - - -
Home page - https://snakemake.readthedocs.io/en/stable/ -
Community workflows page - https://github.com/snakemake-workflows -
- - - -## Extra KNIME (.knwf) information {#knime} - - - - - - - - - - - -
Home page - - https://www.knime.com/ -
- Community workflows page - - https://hub.knime.com/ -
+{% include glossary.html %} diff --git a/docs/guide-to-using-workflowhub.md b/docs/guide-to-using-workflowhub.md index d4f148c..32e6723 100644 --- a/docs/guide-to-using-workflowhub.md +++ b/docs/guide-to-using-workflowhub.md @@ -1,5 +1,7 @@ --- title: A guide to using WorkflowHub +description: A detailed guide that can be further tailored to support research projects, organisations and initiatives that would like to use WorkflowHub. +page_id: guide --- **If your research project is producing workflows, they should be registered in WorkflowHub:** diff --git a/docs/how-to-register.md b/docs/how-to-register.md index 4aff2a2..ae27243 100644 --- a/docs/how-to-register.md +++ b/docs/how-to-register.md @@ -3,38 +3,35 @@ title: How to register redirect_from: /How-to-register/ --- -> Which WorkflowHub instance? -> * Use for testing - this _testing instance_ may occasionally be wiped -> * Use for actual workflow registrations - this is the _production instance_ -In order to register yourself in WorkflowHub, you need to click Register button in the top right hand corner of WorkflowHub. +1. In order to register yourself in WorkflowHub, you need to click Register button in the top right hand corner of WorkflowHub. You can also visit [this link](https://workflowhub.eu/signup). +2. You will then see a wizard, where you are prompted to provide: + * A Login name: this can be your real name, or another appropriate name. + * An email address + * A password for your account -![]({{ '/images/register-1.PNG' | relative_url }}) +{:start="3"} -It will take you to a screen where you need to provide +3. When complete, click the `Register` button in the bottom left hand corner. +4. You will then be taken to a screen where you can enter further information (see figure below). +5. WorkflowHub requires the following information: + * First Name + * Last Name + * Your email address (this is automatically populated from the previous screen) -* A Login name (can be your real name, or another appropriate name) -* An email address -* A password for your account. When complete click the Register button in the bottom left hand corner. +{:start="6"} -![]({{ '/images/register-2.PNG' | relative_url }}) +6. It is recommended that you also add an ORCID ID. If you do not have an ORCID, you can register for one at . -You will then be taken to a screen where you will enter further information. We require the following information: +{% include callout.html type="tip" content="Information that is required is indicated with a red star." %} -* First Name -* Last Name -* Your email address, which should be automatically populated from the previous screen. +{:start="7"} -It is recommended that you also add +7. If your project (i.e. Team) is already in WorkflowHub, please select it from the dropdown menu. +8. If your institution (i.e. Organisation) is already in WorkflowHub, please select it from the dropdown menu. +9. After you have registered the rest of your information, you will need to activate your account. You will receive an email in the account you have provided. -* ORCID ID - if you do not have an ORCID you will need to register for one at +{% include callout.html type="note" content="If you don't join any listed Team during registration, you can request to join a Team or create your own Team after the registration." %} -Information that is required is indicated with a red star. +![]({{ '/images/register-3.PNG' | relative_url }}) -If your project is already in WorkflowHub please select it from the dropdown menu. If your institute is already in WorkflowHub please select it from the dropdown menu. - -If you don't join any listed project during registration, you can request to join a project or create your own project after the registration. - -![]({{ '/images/register-3.PNG' | relative_url }}) - -After you have registered the rest of your information, you will need to activate your account. You will receive an email in the email account you have provided. diff --git a/docs/index.md b/docs/index.md index 9f26c4f..9ba06b1 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,6 +1,6 @@ --- -title: Documentation -toc: false +title: Getting started with WorkflowHub +description: How to get started with WorkflowHub, including a quick start guide for registering workflows. page_id: docs redirect_from: - /docs/before-you-start/ @@ -8,6 +8,10 @@ redirect_from: - /docs/getting-started/ --- +## What information would you like to view? + +{% include section-navigation-tiles.html custom="guide, finding, instances, organising, registering, maintaining, citable, developer, metadata, glossary" sort=false %} + ## Quick start guide @@ -17,7 +21,7 @@ redirect_from: ### 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. +Register on the [sign up page](https://workflowhub.eu/signup) 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 @@ -31,8 +35,7 @@ You can request to create a `Team` in any or all of the following `Spaces`: * [**Australian BioCommons**](https://workflowhub.eu/programmes/8) * [**BioExcel**](https://workflowhub.eu/programmes/2) * [**EOSC-Life**](https://workflowhub.eu/programmes/6) -- [**A new space**](https://workflowhub.eu/programmes/new): if a pre-existing space is not suitable, you can create a space - * This is a good option if you represent a group, consortium, or community where multiple teams might want to register with WorkflowHub +- [**A new space**](https://workflowhub.eu/programmes/new): if a pre-existing space is not suitable, you can create a space. This is a good option if you represent a group, consortium, or community where multiple teams might want to register with WorkflowHub {% include image.html file="spaces.svg" caption="Fig 1. Left - the relationship between the structural elements of WorkflowHub: Spaces, Teams and workflows. Right - examples of where you can create your new team on WorkflowHub." alt="Spaces and teams explained" %} @@ -41,18 +44,15 @@ You can request to create a `Team` in any or all of the following `Spaces`: ### 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. +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. More information on how to join a team can be found on the [how to create and join teams and spaces page](/docs/join-create-teams-spaces) -More information on how to join a team can be found on the [how to create and join teams and spaces](/docs/join-create-teams-spaces) {% include callout.html type="important" content="if you are creating a team, make sure the team name is descriptive." %} - **Figure 2** shows the minimum information required for a new team, which includes: - **Space** - the space you selected or created in step 2 above - **Team name** -- **Team organization** - the organization that should be linked to your team on WorkflowHub. e.g. `University of Melbourne` - * If your organization is not yet on WorkflowHub, you can [create an organization](https://workflowhub.eu/institutions/new) +- **Team organization** - the organization that should be linked to your team on WorkflowHub (e.g. `University of Melbourne`). If your organization is not yet on WorkflowHub, you can [create an organization](https://workflowhub.eu/institutions/new) {% include callout.html type="important" content="you can add multiple organizations to both your profile and teams on WorkflowHub." %} @@ -61,8 +61,6 @@ More information on how to join a team can be found on the [how to create and jo ### 4. Register workflow(s) -Workflows can be registered using the [WorkflowHub wizard](https://workflowhub.eu/workflows/new) - -There is an extensive guide to the [workflow registration process](/docs/registering_workflows/registering-a-workflow/) available in the WorkflowHub documentation. +Workflows can be registered using the [WorkflowHub wizard](https://workflowhub.eu/workflows/new). There is an extensive guide to the [workflow registration process](/docs/registering_workflows/registering-a-workflow/) available in the WorkflowHub documentation. -{% include callout.html type="important" content="We recommend importing a git repository (e.g. GitHub), since WorkflowHub is a hub / registry and not a repository." %} +{% include callout.html type="important" content="importing a git repository (e.g. GitHub) is recommended, since WorkflowHub is a hub / registry and not a repository." %} diff --git a/docs/join-create-teams-spaces.md b/docs/join-create-teams-spaces.md index 1259f7c..b0e2194 100644 --- a/docs/join-create-teams-spaces.md +++ b/docs/join-create-teams-spaces.md @@ -5,21 +5,13 @@ redirect_from: - /joining-a-team --- -When you have registered and logged in, the next step is to either create, or join, a **Team**. To do this, you need to have either selected, or created, both a **Space** and an **Organisation**. This page provides additional details for each of these concepts. - - -## Terminology - -For a description of `Spaces`, `Teams` and `Organisations` please [see this page](/docs/space-team-organisation.md). - -{% include image.html file="spaces_teams_organizations.png" caption="Fig 1. Structure of spaces, teams and organizations. Note that there is flexibility in how spaces are structured, and that you can be part of multiple Spaces, Teams and Organizations." %} +When you have registered and logged in, the next step is to either create, or join, a **`Team`**. To do this, you need to have either selected, or created, both a **`Space`** and an **`Organisation`**. For a description of `Spaces`, `Teams` and `Organisations` please [see this page](/docs/space-team-organisation.md). ## Would you like to join a Team? You can join one or more existing Teams by: -