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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.5.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
vagkaratzas
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vagkaratzas
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Left comments to revise. In addition:
- when staging files, and before commiting them, run
pre-commitlocally so formatting issues are tackled there - make sure
nf-core subworkflows lintcommand passes all test for this subworkflow - Run the
nf-test test /path/to/test/main.nf.test --profile +singularity --verbosecommand twice; one to generate the snapshot, and then once more to make sure the snapshot is not changing.
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| authors: | ||
| - "@vagkaratzas" | ||
| - "@Muskan-2464 |
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| - "@Muskan-2464 | |
| - "@Muskan-2464" |
| description: TSV file containing InterProScan functional annotation results. | ||
| Structure: [ val(meta), path(tsv) ] |
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| description: TSV file containing InterProScan functional annotation results. | |
| Structure: [ val(meta), path(tsv) ] | |
| description: | | |
| TSV file containing InterProScan functional annotation results. | |
| Structure: [ val(meta), path(tsv) ] |
Structure must be part of the description
| description: File containing software versions for all tools used in the workflow. | ||
| Structure: [ path(versions.yml) ] |
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| description: File containing software versions for all tools used in the workflow. | |
| Structure: [ path(versions.yml) ] | |
| description: | | |
| File containing software versions for all tools used in the workflow. | |
| Structure: [ path(versions.yml) ] |
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| name: functional_annotation | |||
| description: Performs functional annotation of protien sequences | |||
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| description: Performs functional annotation of protien sequences | |
| description: Performs functional annotation of protein sequences |
| when { | ||
| workflow { | ||
| """ | ||
| input[0] = Channel.of([ |
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| input[0] = Channel.of([ | |
| input[0] = channel.of([ |
new strict syntax
| // ------------------------------------------------------- | ||
| // TEST 1: Skip InterProScan (safest for CI, no DB needed) | ||
| // ------------------------------------------------------- |
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| // ------------------------------------------------------- | |
| // TEST 1: Skip InterProScan (safest for CI, no DB needed) | |
| // ------------------------------------------------------- |
| // ------------------------------------------------------- | ||
| // TEST 1: Skip InterProScan (safest for CI, no DB needed) | ||
| // ------------------------------------------------------- | ||
| test("fasta - skip_interproscan true") { |
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| test("fasta - skip_interproscan true") { | |
| test("faa - functional annotation) { |
| assertAll( | ||
| { assert workflow.success }, | ||
| { assert workflow.out.interproscan_tsv == [] }, | ||
| { assert snapshot(workflow.out.versions).match("versions_skip") } |
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Update this block to mathc the new test. CHeck the nf-test of domain annotation local subworkflow for inspiration
| // ------------------------------------------------------- | ||
| // TEST 2: Stub run with skip=false (no real DB download) | ||
| // ------------------------------------------------------- | ||
| test("stub run - skip interproscan") { |
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Either remove this second test, or run it with skip_interproscan true, but dont name it stub. (we already have a stub one after)
| assertAll( | ||
| { assert workflow.success }, | ||
| { assert workflow.out.interproscan_tsv == [] }, | ||
| { assert workflow.out.versions == [] } | ||
| ) |
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Update the assertion to more nf-core like ones; see the other local subworkflows of the pipeline
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| nextflow_workflow { | |||
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| name "Test Workflow FUNCTIONAL_ANNOTATION" | |||
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| name "Test Workflow FUNCTIONAL_ANNOTATION" | |
| name "Test Subworkflow FUNCTIONAL_ANNOTATION" |
3 participants
PR checklist
nf-core pipelines lint).nf-test test */local --profile=~test,dockerfor all new local tests).nf-test test */local --profile=~test,docker,debug).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).