GraphQL Workflow Submission Tutorial
Please Note:
This is an advanced feature. Please familiarize yourself with the GraphQL API Documentation before continuing with this tutorial.
Overview
Submitting a workflow execution via the GraphQL API is done in multiple steps. It is expected that this will be done programmatically and not manually. Many id's will be fetched and used in the submission process so simply copying and pasting the values will likely result in user error.
Steps:
- Query for pipelines
- Query specific pipeline information
- Query Project information
- Query Sample and File data from Project
- Submit a Workflow Execution using the information queried in the previous steps
Please note: All values fetched by executing these queries are unique to your database. Copying and Pasting the commands without replacing the values with your own id's will not work.
1. Query for pipelines
Query the list of pipelines to find the one you want to use.
query getPipelines {
pipelines(workflowType: "available"){
name
version
}
}
Result
{
"data": {
"pipelines": [
{
"name": "phac-nml/iridanextexample",
"version": "1.0.3"
},
{
"name": "phac-nml/iridanextexample",
"version": "1.0.2"
},
{
"name": "phac-nml/iridanextexample",
"version": "1.0.1"
},
{
"name": "phac-nml/iridanextexample",
"version": "1.0.0"
}
]
}
}
The name and version fields will be used in the next step. In this example version 1.0.3.
2. Query for Pipeline Information
We are able to get all the information about a pipeline with this query.
query getPipelineInfo {
pipeline(workflowName:"phac-nml/iridanextexample",workflowVersion:"1.0.3"){
automatable
description
executable
metadata
name
version
workflowParams
}
}
Result:
{
"data": {
"pipeline": {
"automatable": false,
"description": "IRIDA Next Example Pipeline",
"executable": true,
"metadata": {
"workflow_name": "phac-nml/iridanextexample",
"workflow_version": {
"name": "1.0.3"
}
},
"name": "phac-nml/iridanextexample",
"version": "1.0.3",
"workflowParams": {
"input_output_options": {
"title": "Input/output options",
"description": "Define where the pipeline should find input data and save output data.",
"properties": {
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"schema": {
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/phac-nml/iridanextexample/main/assets/schema_input.json",
"title": "phac-nml/iridanextexample pipeline - params.input schema",
"description": "Schema for the file provided with params.input",
"type": "array",
"items": {
"type": "object",
"properties": {
"sample": {
"type": "string",
"pattern": "^\\S+$",
"meta": [
"id"
],
"unique": true,
"errorMessage": "Sample name must be provided and cannot contain spaces"
},
"fastq_1": {
"type": "string",
"pattern": "^\\S+\\.f(ast)?q(\\.gz)?$",
"errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have the extension: '.fq', '.fastq', '.fq.gz' or '.fastq.gz'"
},
"fastq_2": {
"errorMessage": "FastQ file for reads 2 cannot contain spaces and must have the extension: '.fq', '.fastq', '.fq.gz' or '.fastq.gz'",
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.f(ast)?q(\\.gz)?$"
},
{
"type": "string",
"maxLength": 0
}
]
}
},
"required": [
"sample",
"fastq_1"
]
}
},
"description": "Path to comma-separated file containing information about the samples in the experiment.",
"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.",
"fa_icon": "fas fa-file-csv",
"required": false
},
"project_name": {
"type": "string",
"default": "assembly",
"pattern": "^\\S+$",
"description": "The name of the project.",
"fa_icon": "fas fa-tag",
"required": false
},
"assembler": {
"type": "string",
"default": "stub",
"fa_icon": "fas fa-desktop",
"description": "The sequence assembler to use for sequence assembly.",
"enum": [
"default",
"stub",
"experimental"
],
"required": false
},
"random_seed": {
"type": "integer",
"default": 1,
"fa_icon": "fas fa-dice-six",
"description": "The random seed to use for sequence assembly.",
"minimum": 1,
"required": false
}
}
}
}
}
}
}
The output informs us of the structure of the fields we will provide to run the pipeline.
Specifically, We will be using the following fields from the result
workflowNameworkflowVersionworkflowParamsassemblerrandom_seedproject_name
The output also informs us of the structure for the samplesWorkflowExecutionAttributes (sample_id) and samplesheet_params (sample, fastq_1, fastq_2) in our final submission query.
3. Query Project information
Query to find the Project containing the samples you want to use in the pipeline. In this example we are simply getting the first project.
query getProjects {
projects(first: 1){
nodes{
fullName
id
fullPath
}
}
}
Result
{
"data": {
"projects": {
"nodes": [
{
"fullName": "Borrelia / Borrelia burgdorferi / Outbreak 2024",
"id": "gid://irida/Project/2bd03791-2213-444d-8df3-fdda40fc262a",
"fullPath": "borrelia/borrelia-burgdorferi/outbreak-2024"
}
]
}
}
}
We will be using the fullPath field in the next step, and id in the final step
4. Query Sample and File data from Project
Using the fullPath from the previous step, we will query for the sample and file information we will use in the pipeline.
Step 2 informed us that for each sample we need:
- the sample
id - the sample
puid, - the file (attachment)
id's
In this example we will only use 1 sample.
query getProjectInfo{
project(fullPath: "borrelia/borrelia-burgdorferi/outbreak-2024") {
samples(first:1){
nodes{
id
puid
attachments{
nodes{
filename
id
}
}
}
}
}
}
Result
{
"data": {
"project": {
"samples": {
"nodes": [
{
"id": "gid://irida/Sample/c9f3806d-4bf1-4462-bc46-7b547338cc11",
"puid": "INXT_SAM_AZCMYRDHEJ",
"attachments": {
"nodes": [
{
"filename": "reference.fasta",
"id": "gid://irida/Attachment/b6ab6077-b3bf-4d5a-ba0c-dc97de7741df"
},
{
"filename": "08-5578-small_S1_L001_R2_001.fastq.gz",
"id": "gid://irida/Attachment/cad0ae33-0c82-4960-8580-92358686609f"
},
{
"filename": "08-5578-small_S1_L001_R1_001.fastq.gz",
"id": "gid://irida/Attachment/f2fad21f-f68f-4871-990f-b47880bed390"
}
]
}
}
]
}
}
}
}
In our example, we are interested in the forward and reverse reads, filenames 08-55...R1...fastq.gz and 08-55...R2...fastq.gz. Take care to note which file id is forward and reverse as the next step will accept them as fastq_1 and fastq_2. The read directions can also be queried from the attachments metadata fields.
5. Submit a Workflow Execution using the information queried in the previous steps
Using all the information gathered in the previous steps, we can now submit our Workflow Execution.
Since this is a Mutation, we also include the workflowExecution and error blocks to see the if our submission succeeded.
mutation submitWorkflowExecution {
submitWorkflowExecution (input:{
name:"My Workflow Submission from GraphQL"
projectId: "gid://irida/Project/2bd03791-2213-444d-8df3-fdda40fc262a"
updateSamples: false
emailNotification: false
workflowName: "phac-nml/iridanextexample"
workflowVersion:"1.0.3"
workflowParams: {
assembler: "stub",
random_seed: 1,
project_name: "assembly"
}
samplesWorkflowExecutionsAttributes:[
{
sample_id:"gid://irida/Sample/c9f3806d-4bf1-4462-bc46-7b547338cc11"
samplesheet_params:{
sample: "INXT_SAM_AZCMYRDHEJ",
fastq_1:"gid://irida/Attachment/f2fad21f-f68f-4871-990f-b47880bed390",
fastq_2:"gid://irida/Attachment/cad0ae33-0c82-4960-8580-92358686609f"
}
}
]
}){
workflowExecution{
name
state
id
}
errors{
message
path
}
}
}
Result
{
"data": {
"submitWorkflowExecution": {
"workflowExecution": {
"name": "My Workflow Submission from GraphQL",
"state": "initial",
"id": "gid://irida/WorkflowExecution/468dcdb5-cf94-4deb-b0b6-67033f156af4"
},
"errors": []
}
}
}
If we now look at the Workflow Executions page in IRIDA Next, we should see our submitted pipeline.