In this project, we will create two simple tools and build a workflow that we can run on ICA using CLI. The first tool (tool-fqTOfa.cwl) will convert a FASTQ file to a FASTA file. The second tool(tool-countLines.cwl) will count the number of lines in an input FASTA file. The workflow (workflow.cwl) will combine the two tools to convert an input FASTQ file to a FASTA file and count the number of lines in the resulting FASTA file.
Following are the two CWL tools and workflow scripts we will use in the project. If you are new to CWL, please refer to the cwl user guide for a better understanding of CWL codes. You will also need the cwltool installed to create these tools and workflows. You can find installation instructions on the CWL github page.
[!IMPORTANT]
Please note that we don't specify the Docker image used in both tools. In such a case, the default behaviour is to use public.ecr.aws/docker/library/bash:5 image. This image contains basic functionality (sufficient to execute wc and awk commands).
In case you want to use a different public image, you can specify it using requirements tag in cwl file. Assuming you want to use *ubuntu:latest' you need to add
In case you want to use a Docker image from the ICA Docker repository, you would need the link to AWS ECR from ICA GUI. Double-click on the image name in the Docker repository and copy the URL to the clipboard. Add the URL to dockerPull key.
To add a custom or public docker image to the ICA repository, please refer to the Docker Repository.
Authentication
Before you can use ICA CLI, you will need to authenticate using the Illumina API key. Please follow these instructions to authenticate.
Enter/Create a Project
You can create a project or use an existing project for creating a new pipeline. You can create a new project using the "icav2 projects create" command.
If you do not provide the "--region" flag, the value defaults to the existing region when there is only one region available. When there is more than one region available, a selection must be made from the available regions at the command prompt. The region input can be determined by calling the "icav2 regions list" command first.
You can select the project to work on by entering the project using the "icav2 projects enter" command. Thus, you won't need to specify the project as an argument.
% icav2 projects enter basic-cli-tutorial
You can also use the "icav2 projects list" command to determine the names and ids of the project you have access to.
% icav2 projects list
Create a pipeline on ICA
"projectpipelines" is the root command to perform actions on pipelines in a project. "create" command creates a pipeline in the current project.
The parameter file specifies the input for the workflow with additional parameter settings for each step in the workflow. In this tutorial, input is a FASTQ file shown inside <dataInput> tag in the parameter file. There aren't any specific settings for the workflow steps resulting in a parameter file below with an empty <steps> tag. Create a parameter file (parameters.xml) with the following content using a text editor.
The following command creates a pipeline called "cli-tutorial" using the workflow "workflow.cwl", tools "tool-fqTOfa.cwl" and "tool-countLines.cwl" and parameter file "parameter.xml" with small storage size.
Once the pipeline is created, you can view it using the "list" command.
% icav2 projectpipelines list
ID CODE DESCRIPTION
6779fa3b-e2bc-42cb-8396-32acee8b6338 cli-tutorial cli tutorial pipeline
Running the pipeline
Upload data to the project using the "icav2 projectdata upload" command. Please refer to the Data page for advanced data upload features. For this test, we will use a small FASTQ file test.fastq containing the following reads.
The "icav2 projectdata upload" command lets you upload data to ica.
% icav2 projectdata upload test.fastq /
oldFilename= test.fastq en newFilename= test.fastq
bucket= stratus-gds-use1 prefix= 0a488bb2-578b-404a-e09d-08d9e3343b2b/test.fastq
Using: 1 workers to upload 1 files
15:23:32: [0] Uploading /Users/user1/Documents/icav2_validation/for_tutorial/working/test.fastq
15:23:33: [0] Uploaded /Users/user1/Documents/icav2_validation/for_tutorial/working/test.fastq to /test.fastq in 794.511591ms
Finished uploading 1 files in 795.244677ms
The "list" command lets you view the uploaded file. Note the ID of the file you want to use with the pipeline.
% icav2 projectdata list
PATH NAME TYPE STATUS ID OWNER
/test.fastq test.fastq FILE AVAILABLE fil.c23246bd7692499724fe08da020b1014 4b197387-e692-4a78-9304-c7f73ad75e44
The "icav2 projectpipelines start" command initiates the pipeline run. The following command runs the pipeline. Note the id for exploring the analysis later.
Note: If for some reason your "create" command fails and needs to rerun, you might get an error (ConstraintViolationException). If so, try your command with a different name.
The pipelines can be run using JSON input type as well. The following is an example of running pipelines using JSON input type. Note that JSON input works only with file-based CWL pipelines (built using code, not a graphical editor in ICA).
runtime.ram and runtime.cpu values are by default evaluated using the compute environment running the host CWL runner. CommandLineTool Steps within a CWL Workflow run on different compute environments than the host CWL runner, so the valuations of the runtime.ram and runtime.cpu for within the CommandLineTool will not match the runtime environment the tool is running in. The valuation of runtime.ram and runtime.cpu can be overridden by specifying cpuMin and ramMin in the ResourceRequirements for the CommandLineTool.
