-
Notifications
You must be signed in to change notification settings - Fork 26
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
2 changed files
with
191 additions
and
40 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,151 @@ | ||
| # Setup Method | ||
|
|
||
| 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. | ||
|
|
||
| ## Syntax | ||
|
|
||
| The setup method is typically used within the context of a test case. The basic syntax for the setup method is as follows: | ||
|
|
||
| ```groovy | ||
| test("my test"){ | ||
| setup { | ||
| // Define and execute dependent processes or workflows here | ||
| } | ||
| } | ||
| ``` | ||
|
|
||
| Within the setup block, you can use the `run` method to define and execute dependent processes or workflows. | ||
|
|
||
| The `run` method syntax for a process is as follows: | ||
|
|
||
| ```groovy | ||
| run("ProcessName") { | ||
| script "path/to/process/script.nf" | ||
| process { | ||
| // Define the process inputs here | ||
| } | ||
| } | ||
| ``` | ||
|
|
||
| The `run` method syntax for a workflow is as follows: | ||
|
|
||
| ```groovy | ||
| run("WorkflowName") { | ||
| script "path/to/workflow/script.nf" | ||
| workflow { | ||
| // Define the workflow inputs here | ||
| } | ||
| } | ||
| ``` | ||
|
|
||
| ## Example Usage | ||
|
|
||
| ### 1. Local Setup Method | ||
|
|
||
| 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." | ||
|
|
||
| ```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() | ||
| } | ||
| } | ||
| } | ||
| ``` | ||
|
|
||
| ### 2. Global Setup Method | ||
|
|
||
| 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. | ||
|
|
||
| ```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() | ||
| } | ||
| } | ||
| } | ||
| ``` |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters