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Enable the execution of dependent modules for generating test data (#127
) * Add `run` method to setup block and fix relativ paths * Add documentation * Update documentation
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| # Setup Method | ||
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| The setup method allows you to specify processes or workflows that need to be executed before the primary `when` block. It serves as a mechanism to prepare the required input data or set up essential steps prior to the primary processing block. | ||
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| ## Syntax | ||
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| The setup method is typically used within the context of a test case. The basic syntax for the setup method is as follows: | ||
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| ```groovy | ||
| test("my test"){ | ||
| setup { | ||
| // Define and execute dependent processes or workflows here | ||
| } | ||
| } | ||
| ``` | ||
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| Within the setup block, you can use the `run` method to define and execute dependent processes or workflows. | ||
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| The `run` method syntax for a process is as follows: | ||
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| ```groovy | ||
| run("ProcessName") { | ||
| script "path/to/process/script.nf" | ||
| process { | ||
| // Define the process inputs here | ||
| } | ||
| } | ||
| ``` | ||
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| The `run` method syntax for a workflow is as follows: | ||
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| ```groovy | ||
| run("WorkflowName") { | ||
| script "path/to/workflow/script.nf" | ||
| workflow { | ||
| // Define the workflow inputs here | ||
| } | ||
| } | ||
| ``` | ||
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| !!! warning | ||
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| Please keep in mind that changes in procsses or workflows, which are executed in the setup method, can result in a failed test run. | ||
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| ## Example Usage | ||
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| ### 1. Local Setup Method | ||
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| In this example, we create a setup method within a Nextflow process definition to execute a dependent process named "ABRICATE_RUN." This process generates input data that is required for the primary process "ABRICATE_SUMMARY." The `setup` block specifies the execution of "ABRICATE_RUN," and the `when` block defines the processing logic for "ABRICATE_SUMMARY." | ||
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| ```groovy | ||
| nextflow_process { | ||
| name "Test process data" | ||
| script "../main.nf" | ||
| process "ABRICATE_SUMMARY" | ||
| config "./nextflow.config" | ||
| test("Should use process ABRICATE_RUN to generate input data") { | ||
| setup { | ||
| run("ABRICATE_RUN") { | ||
| script "../../run/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = Channel.fromList([ | ||
| tuple([ id:'test1', single_end:false ], // meta map | ||
| file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)), | ||
| tuple([ id:'test2', single_end:false ], | ||
| file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true)) | ||
| ]) | ||
| """ | ||
| } | ||
| } | ||
| } | ||
| when { | ||
| process { | ||
| """ | ||
| input[0] = ABRICATE_RUN.out.report.collect{ meta, report -> report }.map{ report -> [[ id: 'test_summary'], report]} | ||
| """ | ||
| } | ||
| } | ||
| then { | ||
| assert process.success | ||
| assert snapshot(process.out).match() | ||
| } | ||
| } | ||
| } | ||
| ``` | ||
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| ### 2. Global Setup Method | ||
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| In this example, a global setup method is defined for all tests within a Nextflow process definition. The setup method is applied to multiple test cases, ensuring consistent setup for each test. This approach is useful when multiple tests share the same setup requirements. | ||
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| ```groovy | ||
| nextflow_process { | ||
| name "Test process data" | ||
| script "../main.nf" | ||
| process "ABRICATE_SUMMARY" | ||
| config "./nextflow.config" | ||
| setup { | ||
| run("ABRICATE_RUN") { | ||
| script "../../run/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = Channel.fromList([ | ||
| tuple([ id:'test1', single_end:false ], // meta map | ||
| file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)), | ||
| tuple([ id:'test2', single_end:false ], | ||
| file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true)) | ||
| ]) | ||
| """ | ||
| } | ||
| } | ||
| } | ||
| test("first test") { | ||
| when { | ||
| process { | ||
| """ | ||
| input[0] = ABRICATE_RUN.out.report.collect{ meta, report -> report }.map{ report -> [[ id: 'test_summary'], report]} | ||
| """ | ||
| } | ||
| } | ||
| then { | ||
| assert process.success | ||
| assert snapshot(process.out).match() | ||
| } | ||
| } | ||
| test("second test") { | ||
| when { | ||
| process { | ||
| """ | ||
| input[0] = ABRICATE_RUN.out.report.collect{ meta, report -> report }.map{ report -> [[ id: 'test_summary'], report]} | ||
| """ | ||
| } | ||
| } | ||
| then { | ||
| assert process.success | ||
| assert snapshot(process.out).match() | ||
| } | ||
| } | ||
| } | ||
| ``` |
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