Restore manifest contributors and round out nf-test coverage#37
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kenibrewer wants to merge 4 commits intoken-brewer/feat-analysisfrom
Open
Restore manifest contributors and round out nf-test coverage#37kenibrewer wants to merge 4 commits intoken-brewer/feat-analysisfrom
kenibrewer wants to merge 4 commits intoken-brewer/feat-analysisfrom
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Add Erin Weisbart and Dave Bunten back as contributors alongside Kenneth Brewer (author, maintainer), with affiliation, email, github, and ORCID filled in. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Each nf-test file now has both stub and real (non-stub) test cases. The real assaydev and analysis tests reference illumination .npy fixtures from s3://nf-core-test-datasets/cellpainting/minimal_dataset (added in nf-core/test-datasets#1606) alongside source images from s3://cellpainting-gallery. The pipeline-level test gains a non-stub variant that runs the full test profile end-to-end. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Merge the real and stub pipeline tests back into tests/default.nf.test (matching nf-core/rnaseq, sarek, and methylseq) and tag the stub variants with stub_test so the fast pre-push command can opt in via --tag stub_test. Update AGENTS.md (CLAUDE.md is a symlink) accordingly. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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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. |
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Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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Summary
nf-testvariants forcellprofiler/assaydevelopment,cellprofiler/analysis, and the pipeline-leveltests/default.nf.test, sourcing illumination.npyfixtures froms3://nf-core-test-datasets/cellpainting/minimal_dataset/...(added in add cellpainting data test-datasets#1606)*.nf.testfile; tag stub variants withstub_testso--tag stub_testkeeps pre-push fast (~3min) while a tag-less run does the full validation (~13min)AGENTS.md/CLAUDE.mdpre-push commands accordinglyTest plan
nf-test test tests/default.nf.test modules/local --profile test,docker --tag stub_test— 5/5 stub tests pass in 126snextflow run . -profile test,docker --outdir resultssucceeds end-to-end (24/24 processes, ~10min)assets/samplesheet.csv