Nextflow runner: remove deprecated map, mapId, mapData, mapPassthrough, renameKeys and DataflowHelper #792
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DriesSchaumont
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DriesSchaumont
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DriesSchaumont
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rcannood
requested changes
Jan 6, 2025
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| // Fetch default values for arguments | ||
| def defaultArgs = config.allArguments | ||
| .findAll { it.containsKey("default") } | ||
| .collectEntries { [ it.plainName, it.default ] } | ||
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Please add an entry to the changelog for this change. Ideally, it'd be a separate PR because it's not related to the removal of previously deprecated arguments ^^
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Added a CHANGELOG entry. I added this change because otherwise the tests were failing. So I would like to avoid a separate PR if possible.
rcannood
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Jan 8, 2025
src/main/resources/io/viash/runners/nextflow/channel/channelFromParams.nf
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src/main/resources/io/viash/runners/nextflow/channel/channelFromParams.nf
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src/test/resources/testnextflowvdsl3/workflows/pipeline3/main.nf
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DriesSchaumont
commented
Jan 8, 2025
| @@ -63,59 +63,6 @@ class Vdsl3ModuleTest extends AnyFunSuite with BeforeAndAfterAll { | |||
| assert(!lines2.isDefined) | |||
| } | |||
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| test("Test map/mapData/id arguments", DockerTest, NextflowTest) { | |||
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This test has an equivalent in NextflowScriptTest
rcannood
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Jan 8, 2025
| entrypoint: run_wf | ||
| platforms: |
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Suggested change
| platforms: | |
| engines: |
?
rcannood
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Jan 8, 2025
src/main/resources/io/viash/runners/nextflow/channel/channelFromParams.nf
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src/test/resources/testnextflowvdsl3/src/test_wfs/empty_workflow/main.nf
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Co-authored-by: Robrecht Cannoodt <[email protected]>
DriesSchaumont
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Jan 8, 2025
src/main/resources/io/viash/runners/nextflow/channel/channelFromParams.nf
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Grifs
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src/main/resources/io/viash/runners/nextflow/channel/channelFromParams.nf
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…omParams.nf Co-authored-by: Hendrik Cannoodt <[email protected]>
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Describe your changes
Remove deprecated map, mapId, mapData, mapPassthrough
Related issue(s)
Closes #xxxxType of Change
Checklist
Requirements:
Tests:
Documentation:
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