Microreact_Export¶
Quick Facts¶
| Workflow Type | Applicable Kingdom | Last Known Changes | Command-line Compatibility | Workflow Level | Dockstore |
|---|---|---|---|---|---|
| Exporting Data from Terra, Standalone | Any taxa | vX.X.X | Yes | Set-level | Microreact_Export_PHB |
Microreact_Export_PHB¶
This workflow allows users to submit Terra data tables as metadata and phylogenetic trees resulting from other Terra run workflows directly to Microreact using their Access Token. A user can also update an existing Microreact project with a new metadata file or additional tree files. If an access token is unavailable users can manually upload the output project file to Microreact.
Microreact_Export Diagram
Updating Projects
When updating an existing project there are a few places to obtain the input for project_url. One place to pull this string from is the web address of the project in your account which will look like this, https://microreact.org/project/<project_url>run.
A second location is within the output of microreact_api_response in the id field.
A third location would be from the My Projects tab. The project id is displayed for each project within your account.
Inputs¶
| Terra Task Name | Variable | Type | Description | Default Value | Terra Status |
|---|---|---|---|---|---|
| wf_microreact_export | id_column | String | Column used as the unique identifier for Microreact | Required | |
| wf_microreact_export | project_name | String | Name of the project to be uploaded to Microreact | Required | |
| wf_microreact_export | set_id | String | ID column of the set being run | Required | |
| wf_microreact_export | terra_project_name | String | Terra project location where metadata Terra table is housed | Required | |
| wf_microreact_export | terra_table_name | String | Name of the Terra table used as the Microreact metadata table | Required | |
| wf_microreact_export | terra_workspace_name | String | Terra workspace location where metadata Terra table is housed | Required | |
| create_microreact_project | cpu | Int | Number of CPUs to allocate to the task | 2 | Optional |
| create_microreact_project | disk_size | Int | Amount of storage (in GB) to allocate to the task | 10 | Optional |
| create_microreact_project | docker | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/theiagen/microreact_export:1.0.0 | Optional |
| create_microreact_project | memory | Int | Amount of memory/RAM (in GB) to allocate to the task | 4 | Optional |
| download_terra_table | cpu | Int | Number of CPUs to allocate to the task | 1 | Optional |
| download_terra_table | disk_size | Int | Amount of storage (in GB) to allocate to the task | 10 | Optional |
| download_terra_table | docker | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21 | Optional |
| download_terra_table | memory | Int | Amount of memory/RAM (in GB) to allocate to the task | 2 | Optional |
| wf_microreact_export | access_token | String | Users token used to upload projects to their Microreact account | Optional | |
| wf_microreact_export | date_column | String | Column within the input Terra table to be used as the date designation | Optional | |
| wf_microreact_export | download_table | Boolean | When true, will download th specified Terra table | True | Optional |
| wf_microreact_export | matrix_files | Array[File] | A list of matrix files a user would like to upload to the Microreact project. Can be written as [this.matrix1, this.matrix2, etc]. | Optional | |
| wf_microreact_export | metadata_columns | Array[String] | A list of column names from the input Terra table that the user would like to be included in their Microreact metadata table | Optional | |
| wf_microreact_export | metadata_file | File | To be used if a separate metadata TSV is required other than downloading a Terra table | Optional | |
| wf_microreact_export | project_url | String | URL used to update a microreact project. Can be found as the code within the webpage URL. | Optional | |
| wf_microreact_export | remove_file_columns | Boolean | When true, this will remove all columns that contain file opjects to prevent the pushing of Google cloud addresses to the metadata table | True | Optional |
| wf_microreact_export | restricted_access | Boolean | Sets the access level of the project to restricted when true. Only those specifically added will be able to access. | True | Optional |
| wf_microreact_export | tree_files | Array[File] | A list of tree files a user would like to upload to the Microreact project. Can be written as [this.tree1, this.tree2, etc]. | Optional |
Workflow Tasks¶
download_terra_table: Data Retrieval
This task will return a selected Terra table as a TSV file when provided the Terra project, workspace, and table name.
download_terra_table Technical Details
| Links | |
|---|---|
| Task | task_download_terra_table.wdl |
microreact_export: Data Export
This task creates new Microreact projects or updates existing projects using Terra tables as metadata inputs. This is done by accessing Microreact using a user's access token and interacting with Microreact's API to submit created project files directly to Microreact.
If a user does not have an access token they will still receive a finalized project file in JSON format. If a submission to Microreact is attempted a response JSON will be returned to the user for review.
Microreact Export Technical Details
| Links | |
|---|---|
| Task | task_microreact_export.wdl |
Outputs¶
| Variable | Type | Description |
|---|---|---|
| microreact_api_response | File | Result of the Microreact API request |
| microreact_input | File | A project file in JSON format that can be used for manual upload to Microreact |
References¶
Microreact: Argimón S, Abudahab K, Goater R, Fedosejev A, Bhai J, Glasner C, Feil E, Holden M, Yeats C, Grundmann H, Spratt B, Aanensen D. 30/11/2016. M Gen 2(11): doi:10.1099/mgen.0.000093