ci(nextflow): nf-test infrastructure and GitHub Actions workflow#110
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FIrgolitsch wants to merge 1 commit intopr-n4-bias-fieldfrom
Open
ci(nextflow): nf-test infrastructure and GitHub Actions workflow#110FIrgolitsch wants to merge 1 commit intopr-n4-bias-fieldfrom
FIrgolitsch wants to merge 1 commit intopr-n4-bias-fieldfrom
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Adds end-to-end testing for Nextflow pipelines using nf-test, with all processes invoked in stub mode so tests run without real imaging data. CI: - .github/workflows/nextflow-ci.yml: triggers on workflows/** changes - nf-test.config: root nf-test configuration - tests/nextflow.config: shared test config Tests: - workflows/preproc/tests/preproc_rawtiles.nf.test: stub-run preproc - workflows/preproc/tests/data/session_01/...: minimal tile inputs - workflows/reconst_3d/tests/soct_3d_reconst.nf.test: stub-run reconst - workflows/reconst_3d/tests/data/shifts_xy.csv: minimal shifts CSV Pipelines: - workflows/preproc/preproc_rawtiles.nf: add stub blocks to all processes
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Adds end-to-end testing for Nextflow pipelines using nf-test, with all processes invoked in stub mode so tests run without real imaging data.
Stacked on #109. Base will be retargeted as upstream PRs merge.
CI
.github/workflows/nextflow-ci.yml: triggers onworkflows/**changes (main,dev)nf-test.config: root nf-test configurationtests/nextflow.config: shared test configTests
workflows/preproc/tests/preproc_rawtiles.nf.test\u2014 stub-run preproc pipelineworkflows/preproc/tests/data/session_01/...\u2014 minimal tile inputsworkflows/reconst_3d/tests/soct_3d_reconst.nf.test\u2014 stub-run reconst pipelineworkflows/reconst_3d/tests/data/shifts_xy.csv\u2014 minimal shifts CSVPipelines
workflows/preproc/preproc_rawtiles.nf: addsstub:blocks to all processes