Restructure nf-core/modules repo #2141
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Has anyone ran |
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Doesn't look like Feel free to revert b68b3b7 if that was intentional. |
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Good spot. Why was the |
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Ah, because that file is only used by the Actions CI? |
JoseEspinosa
approved these changes
Oct 4, 2022
maxulysse
approved these changes
Oct 4, 2022
22 tasks
matthdsm
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to matthdsm/nf-core-modules
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Oct 5, 2022
* Move all modules to modules/nf-core/ folder * Move all tests to modules/nf-core/ folder * Replace relative paths in modules test main scripts * Replace relative paths in subworkflow main scripts * Replace relative paths in subworkflow test scripts * Replace paths to tests in test.yml * Standardise path to tests/config to ./tests/config everywhere * Update relative paths in tests * Update paths in pytest_modules.yml Co-authored-by: Edmund Miller <[email protected]>
This was referenced Oct 6, 2022
TomKellyGenetics
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to TomKellyGenetics/nf-core-modules
that referenced
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Oct 11, 2022
TomKellyGenetics
added a commit
to TomKellyGenetics/nf-core-modules
that referenced
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Oct 11, 2022
nf-core#2141 remove files for restructed UniverSC module (avoids duplicate tests)
apeltzer
added a commit
that referenced
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Feb 14, 2023
* initialise template for new module: "universc" * update UniverSC module updates metadata, docker container source, licensing, and citations * update UniverSC module unit tests and documentation * update UniverSC module add inputs, outputs and example calls for UniverSC and Cell Ranger v3.0.2 calls versions for UniverSC and Cell Ranger * initialise template for new module: "universc" * update UniverSC module updates metadata, docker container source, licensing, and citations * update UniverSC module unit tests and documentation * update UniverSC module add inputs, outputs and example calls for UniverSC and Cell Ranger v3.0.2 calls versions for UniverSC and Cell Ranger * resolve formatting issues for UniverSC module * resolve linting errors for UniverSC module * fix test jobs to call UniverSC version without errors * correct configuration for UniverSC test jobs * correct linting errors for UniverSC module * correct docker build files for UniverSC * correct syntax errors in cellranger version call * prettier docs for UniverSC * add output to test data for UniverSC module * update UniverSC module to restructured repo #2141 remove files for restructed UniverSC module (avoids duplicate tests) * define separate outputs for Cell Ranger and UniverSC tests * remove TODO statements and update UniverSC meta.yml defines input and output variables and triggers automated tests * resolve minor linting issues with UniverSC * update paths to UniverSC module in test config * update container versions and tags for UniverSC module * simplifiy container configurations for UniverSC * update configuration for UniverSC tests (build Cell Ranger transcriptome reference first) * test UniverSC module with Cell Ranger references * update tests for UniverSC for restructured repository * update reference inputs for UniverSC module * set up references for cellranger OS test * resolve permissions errors for starting UniverSC * update input arguments for UniverSC and Cell Ranger OS (tests passing) * correct versions and checksums for UniverSC tests * resolves linting issues for UniverSC * resolves linting issues for UniverSC * update expected test outputs for UniverSC tests * migrate UniverSC tests to calling open source Cell Ranger uses Cell Ranger 3.0.2 OS implementation (MIT License) tests passing locally * migrate changes to source code to updated UniverSC container * update unit tests for UniverSC to correct output (using new container) * update output criteria for UniverSC unit tests * change output directory for UniverSC unit tests * test adding podman to GitHub actions (will revert if reviewers object to it) * correct test errors for Cell Ranger OS tests (UniverSC module) * array format for test checks (UniverSC and Cell Ranger OS) * remove unncessary files from UniverSC module * remove podman from automated testing * remove mentions of nf-core/universc container * call executable script from PATH in UniverSC container * migrate UniverSC module Cell Ranger OS count own directory * reorganise UniverSC submodules * update process names in UniverSC module for consistency * update formatting for UniverSC tests * update unit tests for UniverSC submodules running Cell Ranger OS 3.0.2 * reorganise UniverSC submodules to fit naming conventions * remove stub from UniverSC for testing * add universc/mkfastq to unit tests * correct syntax in cellranger module files * update expected output for universc and universc/count tests now consistent with cellranger/count module * correct syntax for universc/count meta.yaml (pass linting) * add stub to universc and universc/count * update unit tests for universc module * update unit tests for universc module * update unit tests for universc module * update unit tests for universc module * update universc/mkfastq test to run stub * update universc/mkfastq expected outputs when running stub * remove trailing whitespace (linting error) * restructure UniverSC main module * update configuration to run each UniverSC test once only * correct UniverSC unit test configuration * update name of tools in universc tests configuration * update expected output for Cell Ranger and UniverSC tests * updates unit tests for Cell Ranger and UniverSC uses contain for web summary HTML as suggested by @apeltzer #1706 * updates unit tests for Cell Ranger for web summary HTML * updates unit tests for Cell Ranger for web summary HTML * updates unit tests for Cell Ranger for web summary HTML to use description * correct path to Cell Ranger test output * update container options for run UniverSC with singularity runs without root priviledges in writeable container * migrate UniverSC container to mirrored image at nfcore/universc:1.2.4 adds documentation for image build configuration discussed in #1706 * remove redundant submodules from UniverSC with functions already supported by Cell Ranger module #1706 * migrate UniverSC references to generate by Cell Ranger submodules * update test configuration for universc/launch * update expected outputs for UniverSC to use Cell Ranger references * update expected outputs for UniverSC to use Cell Ranger references * remove UniverSC submodules for mkref and mkgtf (already implement in Cell Ranger module) discussed in #1706 * move universc/launch submodule to universc module * remove tests for UniverSC submodules for mkref and mkgtf (already implement in Cell Ranger module) discussed in #1706 * move tests for universc/launch submodule to universc module * migrate universc/launch submodule to universc module * update paths in unit tests from universc/launch to universc * update documentation for UniverSC module * update paths in test config from universc/launch to universc * restore cellranger module (remove changes from PR 1706) * restore cellranger module (remove changes from PR 1706) * restore cellranger module (remove changes from PR 1706) * update style of documentation to pass linting * add podman to settings and docs (passes local test) * test podman configuration * test podman configuration * restore changes to testing (removes podman discussed in #2675) * restore changes to other modules (removes cellranger discussed in #2646) * update podman settings in UniverSC docs * update podman parameters * update container version for universc to stable release 1.2.5 * remove conda tests for universc (not supported) * update container version for universc to latest release 1.2.5.1 (run tests on pushed version on personal account) * update container version for universc to use nfcore/universc:1.2.5.1 mirror * exit logic for universc module that doesn't support conda consistent with other modules exit logic for modules that dont support conda #2657 * trigger GitHub Actions test for tomkellygenetics/universc:1.2.5.1 * add log files to universc output directory (confirm running subroutines as expected) * correct UniverSC test configuration addresses singularity test issue https://github.com/nf-core/modules/actions/runs/3955706571/jobs/6774566021 * update configuration for singularity in universc tests * test running universc with singularity --fakeroot requires shadow-uidmap::newuidmap installed * update configuration for singularity in universc tests * debug GH Actions configuration for singularity in universc tests * test running singularity with —fakeroot write permissions * test singularity— * revert changes to singularity tests disables singularity for universc (image too large) * update container settings for universc allows running rootless podman or singularity using --runtime crun or --writable-tmpfs apptainer/singularity#3220 * test universc with singularity --writable-tmpfs * revert changes to singularity tests (--writable-tmpfs not supported on GH Actions) * update container settings for universc to call nfcore/universc:1.2.5.1 (pending mirrored version available) * update version in UniverSC citation --------- Co-authored-by: Simon Thomas Kelly <[email protected]> Co-authored-by: Gisela Gabernet <[email protected]> Co-authored-by: TomKellyGenetics <tomkellygenetics@gmail> Co-authored-by: Alexander Peltzer <[email protected]>
sam-white04
pushed a commit
to fulcrumgenomics/nf-core-modules
that referenced
this pull request
Feb 27, 2023
* initialise template for new module: "universc" * update UniverSC module updates metadata, docker container source, licensing, and citations * update UniverSC module unit tests and documentation * update UniverSC module add inputs, outputs and example calls for UniverSC and Cell Ranger v3.0.2 calls versions for UniverSC and Cell Ranger * initialise template for new module: "universc" * update UniverSC module updates metadata, docker container source, licensing, and citations * update UniverSC module unit tests and documentation * update UniverSC module add inputs, outputs and example calls for UniverSC and Cell Ranger v3.0.2 calls versions for UniverSC and Cell Ranger * resolve formatting issues for UniverSC module * resolve linting errors for UniverSC module * fix test jobs to call UniverSC version without errors * correct configuration for UniverSC test jobs * correct linting errors for UniverSC module * correct docker build files for UniverSC * correct syntax errors in cellranger version call * prettier docs for UniverSC * add output to test data for UniverSC module * update UniverSC module to restructured repo nf-core#2141 remove files for restructed UniverSC module (avoids duplicate tests) * define separate outputs for Cell Ranger and UniverSC tests * remove TODO statements and update UniverSC meta.yml defines input and output variables and triggers automated tests * resolve minor linting issues with UniverSC * update paths to UniverSC module in test config * update container versions and tags for UniverSC module * simplifiy container configurations for UniverSC * update configuration for UniverSC tests (build Cell Ranger transcriptome reference first) * test UniverSC module with Cell Ranger references * update tests for UniverSC for restructured repository * update reference inputs for UniverSC module * set up references for cellranger OS test * resolve permissions errors for starting UniverSC * update input arguments for UniverSC and Cell Ranger OS (tests passing) * correct versions and checksums for UniverSC tests * resolves linting issues for UniverSC * resolves linting issues for UniverSC * update expected test outputs for UniverSC tests * migrate UniverSC tests to calling open source Cell Ranger uses Cell Ranger 3.0.2 OS implementation (MIT License) tests passing locally * migrate changes to source code to updated UniverSC container * update unit tests for UniverSC to correct output (using new container) * update output criteria for UniverSC unit tests * change output directory for UniverSC unit tests * test adding podman to GitHub actions (will revert if reviewers object to it) * correct test errors for Cell Ranger OS tests (UniverSC module) * array format for test checks (UniverSC and Cell Ranger OS) * remove unncessary files from UniverSC module * remove podman from automated testing * remove mentions of nf-core/universc container * call executable script from PATH in UniverSC container * migrate UniverSC module Cell Ranger OS count own directory * reorganise UniverSC submodules * update process names in UniverSC module for consistency * update formatting for UniverSC tests * update unit tests for UniverSC submodules running Cell Ranger OS 3.0.2 * reorganise UniverSC submodules to fit naming conventions * remove stub from UniverSC for testing * add universc/mkfastq to unit tests * correct syntax in cellranger module files * update expected output for universc and universc/count tests now consistent with cellranger/count module * correct syntax for universc/count meta.yaml (pass linting) * add stub to universc and universc/count * update unit tests for universc module * update unit tests for universc module * update unit tests for universc module * update unit tests for universc module * update universc/mkfastq test to run stub * update universc/mkfastq expected outputs when running stub * remove trailing whitespace (linting error) * restructure UniverSC main module * update configuration to run each UniverSC test once only * correct UniverSC unit test configuration * update name of tools in universc tests configuration * update expected output for Cell Ranger and UniverSC tests * updates unit tests for Cell Ranger and UniverSC uses contain for web summary HTML as suggested by @apeltzer nf-core#1706 * updates unit tests for Cell Ranger for web summary HTML * updates unit tests for Cell Ranger for web summary HTML * updates unit tests for Cell Ranger for web summary HTML to use description * correct path to Cell Ranger test output * update container options for run UniverSC with singularity runs without root priviledges in writeable container * migrate UniverSC container to mirrored image at nfcore/universc:1.2.4 adds documentation for image build configuration discussed in nf-core#1706 * remove redundant submodules from UniverSC with functions already supported by Cell Ranger module nf-core#1706 * migrate UniverSC references to generate by Cell Ranger submodules * update test configuration for universc/launch * update expected outputs for UniverSC to use Cell Ranger references * update expected outputs for UniverSC to use Cell Ranger references * remove UniverSC submodules for mkref and mkgtf (already implement in Cell Ranger module) discussed in nf-core#1706 * move universc/launch submodule to universc module * remove tests for UniverSC submodules for mkref and mkgtf (already implement in Cell Ranger module) discussed in nf-core#1706 * move tests for universc/launch submodule to universc module * migrate universc/launch submodule to universc module * update paths in unit tests from universc/launch to universc * update documentation for UniverSC module * update paths in test config from universc/launch to universc * restore cellranger module (remove changes from PR 1706) * restore cellranger module (remove changes from PR 1706) * restore cellranger module (remove changes from PR 1706) * update style of documentation to pass linting * add podman to settings and docs (passes local test) * test podman configuration * test podman configuration * restore changes to testing (removes podman discussed in nf-core#2675) * restore changes to other modules (removes cellranger discussed in nf-core#2646) * update podman settings in UniverSC docs * update podman parameters * update container version for universc to stable release 1.2.5 * remove conda tests for universc (not supported) * update container version for universc to latest release 1.2.5.1 (run tests on pushed version on personal account) * update container version for universc to use nfcore/universc:1.2.5.1 mirror * exit logic for universc module that doesn't support conda consistent with other modules exit logic for modules that dont support conda nf-core#2657 * trigger GitHub Actions test for tomkellygenetics/universc:1.2.5.1 * add log files to universc output directory (confirm running subroutines as expected) * correct UniverSC test configuration addresses singularity test issue https://github.com/nf-core/modules/actions/runs/3955706571/jobs/6774566021 * update configuration for singularity in universc tests * test running universc with singularity --fakeroot requires shadow-uidmap::newuidmap installed * update configuration for singularity in universc tests * debug GH Actions configuration for singularity in universc tests * test running singularity with —fakeroot write permissions * test singularity— * revert changes to singularity tests disables singularity for universc (image too large) * update container settings for universc allows running rootless podman or singularity using --runtime crun or --writable-tmpfs apptainer/singularity#3220 * test universc with singularity --writable-tmpfs * revert changes to singularity tests (--writable-tmpfs not supported on GH Actions) * update container settings for universc to call nfcore/universc:1.2.5.1 (pending mirrored version available) * update version in UniverSC citation --------- Co-authored-by: Simon Thomas Kelly <[email protected]> Co-authored-by: Gisela Gabernet <[email protected]> Co-authored-by: TomKellyGenetics <tomkellygenetics@gmail> Co-authored-by: Alexander Peltzer <[email protected]>
anoronh4
pushed a commit
to anoronh4/add_submodule
that referenced
this pull request
Apr 27, 2023
* initialise template for new module: "universc" * update UniverSC module updates metadata, docker container source, licensing, and citations * update UniverSC module unit tests and documentation * update UniverSC module add inputs, outputs and example calls for UniverSC and Cell Ranger v3.0.2 calls versions for UniverSC and Cell Ranger * initialise template for new module: "universc" * update UniverSC module updates metadata, docker container source, licensing, and citations * update UniverSC module unit tests and documentation * update UniverSC module add inputs, outputs and example calls for UniverSC and Cell Ranger v3.0.2 calls versions for UniverSC and Cell Ranger * resolve formatting issues for UniverSC module * resolve linting errors for UniverSC module * fix test jobs to call UniverSC version without errors * correct configuration for UniverSC test jobs * correct linting errors for UniverSC module * correct docker build files for UniverSC * correct syntax errors in cellranger version call * prettier docs for UniverSC * add output to test data for UniverSC module * update UniverSC module to restructured repo nf-core/modules#2141 remove files for restructed UniverSC module (avoids duplicate tests) * define separate outputs for Cell Ranger and UniverSC tests * remove TODO statements and update UniverSC meta.yml defines input and output variables and triggers automated tests * resolve minor linting issues with UniverSC * update paths to UniverSC module in test config * update container versions and tags for UniverSC module * simplifiy container configurations for UniverSC * update configuration for UniverSC tests (build Cell Ranger transcriptome reference first) * test UniverSC module with Cell Ranger references * update tests for UniverSC for restructured repository * update reference inputs for UniverSC module * set up references for cellranger OS test * resolve permissions errors for starting UniverSC * update input arguments for UniverSC and Cell Ranger OS (tests passing) * correct versions and checksums for UniverSC tests * resolves linting issues for UniverSC * resolves linting issues for UniverSC * update expected test outputs for UniverSC tests * migrate UniverSC tests to calling open source Cell Ranger uses Cell Ranger 3.0.2 OS implementation (MIT License) tests passing locally * migrate changes to source code to updated UniverSC container * update unit tests for UniverSC to correct output (using new container) * update output criteria for UniverSC unit tests * change output directory for UniverSC unit tests * test adding podman to GitHub actions (will revert if reviewers object to it) * correct test errors for Cell Ranger OS tests (UniverSC module) * array format for test checks (UniverSC and Cell Ranger OS) * remove unncessary files from UniverSC module * remove podman from automated testing * remove mentions of nf-core/universc container * call executable script from PATH in UniverSC container * migrate UniverSC module Cell Ranger OS count own directory * reorganise UniverSC submodules * update process names in UniverSC module for consistency * update formatting for UniverSC tests * update unit tests for UniverSC submodules running Cell Ranger OS 3.0.2 * reorganise UniverSC submodules to fit naming conventions * remove stub from UniverSC for testing * add universc/mkfastq to unit tests * correct syntax in cellranger module files * update expected output for universc and universc/count tests now consistent with cellranger/count module * correct syntax for universc/count meta.yaml (pass linting) * add stub to universc and universc/count * update unit tests for universc module * update unit tests for universc module * update unit tests for universc module * update unit tests for universc module * update universc/mkfastq test to run stub * update universc/mkfastq expected outputs when running stub * remove trailing whitespace (linting error) * restructure UniverSC main module * update configuration to run each UniverSC test once only * correct UniverSC unit test configuration * update name of tools in universc tests configuration * update expected output for Cell Ranger and UniverSC tests * updates unit tests for Cell Ranger and UniverSC uses contain for web summary HTML as suggested by @apeltzer nf-core/modules#1706 * updates unit tests for Cell Ranger for web summary HTML * updates unit tests for Cell Ranger for web summary HTML * updates unit tests for Cell Ranger for web summary HTML to use description * correct path to Cell Ranger test output * update container options for run UniverSC with singularity runs without root priviledges in writeable container * migrate UniverSC container to mirrored image at nfcore/universc:1.2.4 adds documentation for image build configuration discussed in nf-core/modules#1706 * remove redundant submodules from UniverSC with functions already supported by Cell Ranger module nf-core/modules#1706 * migrate UniverSC references to generate by Cell Ranger submodules * update test configuration for universc/launch * update expected outputs for UniverSC to use Cell Ranger references * update expected outputs for UniverSC to use Cell Ranger references * remove UniverSC submodules for mkref and mkgtf (already implement in Cell Ranger module) discussed in nf-core/modules#1706 * move universc/launch submodule to universc module * remove tests for UniverSC submodules for mkref and mkgtf (already implement in Cell Ranger module) discussed in nf-core/modules#1706 * move tests for universc/launch submodule to universc module * migrate universc/launch submodule to universc module * update paths in unit tests from universc/launch to universc * update documentation for UniverSC module * update paths in test config from universc/launch to universc * restore cellranger module (remove changes from PR 1706) * restore cellranger module (remove changes from PR 1706) * restore cellranger module (remove changes from PR 1706) * update style of documentation to pass linting * add podman to settings and docs (passes local test) * test podman configuration * test podman configuration * restore changes to testing (removes podman discussed in nf-core/modules#2675) * restore changes to other modules (removes cellranger discussed in nf-core/modules#2646) * update podman settings in UniverSC docs * update podman parameters * update container version for universc to stable release 1.2.5 * remove conda tests for universc (not supported) * update container version for universc to latest release 1.2.5.1 (run tests on pushed version on personal account) * update container version for universc to use nfcore/universc:1.2.5.1 mirror * exit logic for universc module that doesn't support conda consistent with other modules exit logic for modules that dont support conda nf-core/modules#2657 * trigger GitHub Actions test for tomkellygenetics/universc:1.2.5.1 * add log files to universc output directory (confirm running subroutines as expected) * correct UniverSC test configuration addresses singularity test issue https://github.com/nf-core/modules/actions/runs/3955706571/jobs/6774566021 * update configuration for singularity in universc tests * test running universc with singularity --fakeroot requires shadow-uidmap::newuidmap installed * update configuration for singularity in universc tests * debug GH Actions configuration for singularity in universc tests * test running singularity with —fakeroot write permissions * test singularity— * revert changes to singularity tests disables singularity for universc (image too large) * update container settings for universc allows running rootless podman or singularity using --runtime crun or --writable-tmpfs apptainer/singularity#3220 * test universc with singularity --writable-tmpfs * revert changes to singularity tests (--writable-tmpfs not supported on GH Actions) * update container settings for universc to call nfcore/universc:1.2.5.1 (pending mirrored version available) * update version in UniverSC citation --------- Co-authored-by: Simon Thomas Kelly <[email protected]> Co-authored-by: Gisela Gabernet <[email protected]> Co-authored-by: TomKellyGenetics <tomkellygenetics@gmail> Co-authored-by: Alexander Peltzer <[email protected]>
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