Continuation of #3083 #3456
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Continuation of #3083 #3456
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Strangely it is passing at the moment, it seems the install command returns a passing exit code regardless of installing all modules. - Addresses sanger-tol#2
This reverts commit 534da92.
tests: Add test case for cross-organization subwf
fix: Avoid duplicate downloads in nested subworkflows
* dev: (299 commits) Update nf_core/pipelines/create/utils.py [automated] Update CHANGELOG.md allow numbers in custom pipeline name [automated] Update CHANGELOG.md Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 Fixed linting Updated changelog Added process_high_memory to create/lint list update chagelog use pathlib instead of os.path Apply suggestions from code review add option to skip code linters Update gitpod/workspace-base Docker digest to f189a41 Update pre-commit hook pre-commit/mirrors-mypy to v1.11.0 [automated] Update CHANGELOG.md Update python:3.12-slim Docker digest to 740d94a Update .pre-commit-config.yaml Update nf_core/__main__.py Add default version Automatically add a default version in pipelines_create ...
* dev: (35 commits) don't remove creating a pipeline to test it 😶 update textual snapshots update textual snapshots fix indentation Update nf_core/pipelines/create/create.py [automated] Update CHANGELOG.md [automated] Update CHANGELOG.md add option to exclude changelog from custom pipeline template add option to exclude codespaces from pipeline template remove multiqc images from the template docs and the same for subworkflows run tests also after pytest-migrate update textual snapshots add multiqc potion to test data update textual snapshots fix tests [automated] Update CHANGELOG.md add option to exclude multiqc from pipeline template rename regenerae-snapshots to update-textual-snapshots Apply suggestions from code review ...
…ge_get Use the power of get to skip if tests
Co-authored-by: Matthieu Muffato <[email protected]>
refact: Change function structure to use dicts not lists
* upstream/dev: (45 commits) Apply suggestions from code review update textual snapshot add option to exclude adaptivecard and slackreport from pipeline template update pytest test_make_pipeline_schema [automated] Update CHANGELOG.md add option to exclude email from pipeline template update textual snapshots Update nf_core/pipelines/create/templatefeatures.yml [automated] Update CHANGELOG.md add option to exclude license from pipeline template [automated] Update CHANGELOG.md Update python:3.12-slim Docker digest to 59c7332 [automated] Update CHANGELOG.md Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.0 Ran pre commit add matthias' suggestion woops Overwrite the verbose in ctx in case the user uses it Overwrite the verbose in ctx in case the user uses it Add a verbose click option run prettier on the pipeline output directory ...
* upstream/dev: (120 commits) markdown header add .gitignore to base required files update textual snapshots don't remove .gitignore when unselecting github update textual snapshots some more minimal template fixes udpate changelog handle cases where the directory path contains the name of the component switch to os.walk to support <3.10 versions of Python fix pipeline linting when skipping nf_schema update test to use template_features.yml and add missing files to a feature group rename templatefeatures.yml to template_features.yml update changelog fix linting add tests to ensure all files are part of a template customisation group add process cpus, memory and time to nextflow.config if we remove base.config update textual snapshots Revert "don't remove base.config when removing nf-core components" don't remove base.config when removing nf-core components apply review comments from @mashehu ...
* upstream/dev: Move if statements to top of YAML blocks Don't look for dev, look for not master Remove tests involving environment.yml with 'name' Remove name from conda enviroment.yml in module template Don't test conda `environment.yml` `name` attribute (which should no longer be there) Update CHANGELOG.md Add --update-all flag to remove defaults channels dependents add a tabix tabix test pre commit fix issue where tool and subtool have the same name udpate changelog run nf-core lint --release on PRs to master
refact: Add suggestions from second review
Co-authored-by: Júlia Mir Pedrol <[email protected]>
* test: Add test for installing a module already installed from different org * fix: Remove unnecessary install command * test: Add test for updating cross-org subwfs * fix: Change hash to sha * fix: Add remote url * refact: Create shared instance of subworkflowinstall * test: to keep same named cross mods post subwf rm * refact: Don't use sha for the alternative repo * fix: Add else to sha check * fix: Move check to cross-org stuff * refact: Reverse check order * test: Add update test (#19) * wip: Add bug two * refact: Try defaulting to a dict * fix: Dont allow remote to be unbound * refact: Check if not equal to component type * refact: Re-add isinstance dict * fix: Remove mention of component_name * refact: Add special case for strings following dicts * test: Try removing branch from test case * refact: Remove isinstance for str * refact: Use dict only with get_comps out * Revert "refact: Use dict only with get_comps out" This reverts commit 7ebc6dc. * refact: Check if content has subwfs * refact: Always set current remote * refact: Check sha before resetting current_repo * refact: Do the negative test * refact: Use another variable for remote * refact: Simplify check * refact: Expand check once again * refact: Roll back to previous check * fix: self.sha must not be none to reset to none * Revert "fix: self.sha must not be none to reset to none" This reverts commit 65aa1c4. * Try removing the section entirely * refact: Try moving check to reset * refact: Remove unnecessary current_sha * refact: Change check in get_comps * refact: Set git remote beforehand * refact: Change indent so previous check is the same * refact: Remove current repo check * Revert "refact: Remove current repo check" This reverts commit a956e04. * refact: Try using name list * fix: Remove break in loop * refactor: Always set current_repo * fix: Check if name is in updated * refactor: Remove unused sections and logs * test: Use the same subworkflow in all test cases get_genome_annotation is not necessary, given we're using another subworkflow for the other tests * refact: Update cross_org remote to nf-core-test * fix: Change remote name in install test * refact: Remove none check from all_subworkflows Co-authored-by: Matthieu Muffato <[email protected]> * docs: Add hash comment * refact: Use mod/subwf_name in both sections * test: Check updated subwf content --------- Co-authored-by: Matthieu Muffato <[email protected]>
* write only relevant fields in `.nf-core.yml` * switch from docstrings to Field descsriptions * [automated] Update CHANGELOG.md * update test to new error * second attempt to add ro crates * fix import * first running version * restructure code and add tests * add missing dep * add recommendations from comments * add git contributors * fix filename for CI * better help hint message * fix class name * add correct parent directory to faked crate * add empty ro-crate after sync * fix tests * fix ci test * use github to guess author name, set names as ids if no orcid * add bioschemas, datecreated and datemodified (only set to current time atm) * follow `ComputationalWorkflow` schema for main entitty. * fix date created field * add "about" field to workflow diagram * add input as separate entity * add version to main entity * fix incorrect type * switch to add_workflow method to add main entity and add components as datasets with descriptions * ro_crate -> rocrate * allow mixed list and dict in lint config * nested too deeply * [automated] Update CHANGELOG.md * use repo2crate to generate the main structure of the crate * chore(deps): update dependency prompt_toolkit to <=3.0.48 * chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.7.0 * chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.12.0 * [automated] Update CHANGELOG.md * [automated] Update CHANGELOG.md * Fix typos * Fix typos (second round) * Undo accidental typos fixes * Fix typos (third round) * Update textual snapshots * chore(deps): update python:3.12-slim docker digest to 032c526 * [automated] Update CHANGELOG.md * handle new nf-core.yml structure * update documentation for `multiqc_config` linting * parse yaml correctly * found a better way to handle the ignore file being None * handle new lint config structure * add tests with different valid yaml structures * use correct profile options for sfw test command * [automated] Update CHANGELOG.md * remove last traces of LintConfigType * fix incorrect type * more type fixes * Update CHANGELOG.md * add all lint tests to config * switch all defaults to None and drop them on dump * Update nf_core/utils.py Co-authored-by: Júlia Mir Pedrol <[email protected]> * Update nf_core/utils.py * drop None values when checking for test names * [automated] Fix code linting * no need for Field value * fix test_lint tests * fix worklfow_dispatch trigger and parse more review comments * [automated] Update CHANGELOG.md * Update pre-commit hook pre-commit/mirrors-mypy to v1.13.0 * chore(deps): update github actions * [automated] Update CHANGELOG.md * remove outdated file * Revert "Add new command `nf-core rocrate` to create a Research Object (RO) crate for a pipeline" * move test in correct directory * fix tests * Add seqera containers example * bump ci * Modify test_find_container_images_modules() for Seqera Containers. * Enable Seqera Containers download. * run tests without commiting ro-crate * add ro-crate creation to pipelines create command * fix command import * add rocrate to skip features * remove schema loading, because it is not needed anymore * update snapshots * `modules update`: add a panel around diffs * add `--dir/-d` option to schema commands * [automated] Update CHANGELOG.md * [automated] Update CHANGELOG.md * try to fix coverage report generation * fix test_cli * nf-core download: Fix forgotten symlinks in cache. * try specifying the coverage output file * try naming the files directly * fix variable name * add hiddnen files for upload-artifact action v4 * group diffs by module * Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.1 * [automated] Update CHANGELOG.md * Update GitHub Actions * Ensure that prioritize_direct_download() retains Seqera Singularity Containers and write additional test. * make group border blue * make module names white * Apply suggestions from code review Co-authored-by: Matthias Hörtenhuber <[email protected]> * Add resource limits to Gitpod profile * Update changelog * I fix typos for infrastickers * Fix typo * Update changelog * Update Gitpod to use Miniforge instead of Miniconda * Update Changelog * Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.3 * [automated] Update CHANGELOG.md * handle new schema structure in create-params-file * add tests * [automated] Update CHANGELOG.md * add hint to solve git errors with a synced repo * run pre-commit when testing linting the template pipeline * [automated] Update CHANGELOG.md * [automated] Update CHANGELOG.md * fix template trailing spaces * write proper path and raise a UserWarning to avoid printing the error trace * Apply suggestions from code review Co-authored-by: Matthias Hörtenhuber <[email protected]> * remove logging git error from wrong place * add option to skip .vscode from the template * update textual snapshots * update and fix swf patch tests * Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.4 * [automated] Update CHANGELOG.md * Update codecov/codecov-action action to v5 (#3283) * Update codecov/codecov-action action to v5 * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]> * Update python:3.12-slim Docker digest to 2a6386a (#3284) * Update python:3.12-slim Docker digest to 2a6386a * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]> * apply patch reverse when linting a patched subworkflow * update get_patch_fn to work with subworkflows * move modules_differ.py to components_differ.py * add subworkflows patch missing tests * fix subworkflows update test * update changelog * add help text for --remove flag * apply code review suggestions to patch tests * Update tests/modules/test_patch.py * apply suggestions by @mashehu * remove def from nextflow.config and add trace_report_suffix param * [automated] Update CHANGELOG.md * Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.0 * [automated] Update CHANGELOG.md * add validation.monochromeLogs to config * ignore trace_report_suffix default check * update snapshots * add more tests * enable zip output * Move modules config import after base.config * Update nf_core/pipelines/create/template_features.yml * Update documentation * Update CHANGELOG * Update CHANGELOG.md * Fix linting * Update CHANGELOG * Download: Need to deduplicate Seqera Container matches as well, otherwise a race condition emerges. * Add new function to handle Seqera Container Oras URIs. * Ensure, that oras:// containers are correctly handled. * Download: Add test data for oras:// modules. * Test the new container elimination routine. * Download: Update the tests. * Add dedicated ORAS image format error. * Include oras:// regex in download to recognize the paths. * Changelog. * Update dawidd6/action-download-artifact action to v7 (#3306) * Update dawidd6/action-download-artifact action to v7 * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]> * Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.1 * Update gitpod/workspace-base Docker digest to 12853f7 (#3309) * Update gitpod/workspace-base Docker digest to 12853f7 * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]> * update modules and subworkflows * [automated] Update CHANGELOG.md * also add monochrome_logs if nf-schema is used * add manifest.contributors to nextflow.config * [automated] Update CHANGELOG.md * fix contributors map * Update nf_core/pipeline-template/.github/CONTRIBUTING.md Co-authored-by: Phil Ewels <[email protected]> * Typo in error message. Co-authored-by: Matthias Hörtenhuber <[email protected]> * test also the main sync function itsel * combine json parsing code * loop over list of authors to supply contributors * remove broken test * fix type error * Apply suggestions from code review Co-authored-by: Júlia Mir Pedrol <[email protected]> --------- Co-authored-by: mashehu <[email protected]> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Marcel Ribeiro-Dantas <[email protected]> Co-authored-by: Júlia Mir Pedrol <[email protected]> Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: Matthias Zepper <[email protected]> Co-authored-by: Matthias Zepper <[email protected]> Co-authored-by: Mahesh Binzer-Panchal <[email protected]> Co-authored-by: James A. Fellows Yates <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Phil Ewels <[email protected]> Co-authored-by: Louis LE NEZET <[email protected]> Co-authored-by: Louis Le Nezet <[email protected]> Co-authored-by: LouisLeNezet <[email protected]>
* dev: (458 commits) Apply suggestions from code review fix type error remove broken test loop over list of authors to supply contributors combine json parsing code test also the main sync function itsel Typo in error message. Update nf_core/pipeline-template/.github/CONTRIBUTING.md fix contributors map [automated] Update CHANGELOG.md add manifest.contributors to nextflow.config also add monochrome_logs if nf-schema is used [automated] Update CHANGELOG.md update modules and subworkflows Update gitpod/workspace-base Docker digest to 12853f7 (#3309) Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.1 Update dawidd6/action-download-artifact action to v7 (#3306) Changelog. Include oras:// regex in download to recognize the paths. Add dedicated ORAS image format error. ...
* refact: Use same org_path as modulesrepo first * refact: Change current_remote to a modulesrepo instance * refact: Try using modulesrepo in get_comps * refact: Try using utility functions to grab the yml * fix: Restore old regex behaviour * refact: Use parent path instead of regex in comp_utils * refact: Use modulesrepo for current_repo in install * refact: Move constants to new file and use MRepo Moves constants from component_utils to constants.py so that ModulesRepo can be used from inside of component_utils, thereby avoiding a circular import * Revert "refact: Use modulesrepo for current_repo in install" This reverts commit f4cc0fe. * Reapply "refact: Use modulesrepo for current_repo in install" This reverts commit c5bebcf. * Revert "refact: Move constants to new file and use MRepo" This reverts commit c0a7a00. * refact: Change constants to diff file, use MRepo * fix: Change import in test_update
commit 769f8dd Merge: 5ac5767 d44bcdf Author: Júlia Mir Pedrol <[email protected]> Date: Mon Dec 16 14:23:39 2024 +0100 Merge pull request #3358 from mirpedrol/fix-pre-commit-template Fix pre commit template commit d44bcdf Author: mirpedrol <[email protected]> Date: Mon Dec 16 13:06:36 2024 +0100 more prettier fixes commit 2c78c5e Author: mirpedrol <[email protected]> Date: Mon Dec 16 12:28:59 2024 +0100 more template prittier fixing commit d19e3e0 Author: mirpedrol <[email protected]> Date: Mon Dec 16 12:11:49 2024 +0100 don't try running pre-commit if code-linters or github are not used in the template commit 13e553f Author: mirpedrol <[email protected]> Date: Mon Dec 16 12:08:20 2024 +0100 fix more prettier modifications form the template commit ac703bf Author: mirpedrol <[email protected]> Date: Mon Dec 16 11:58:43 2024 +0100 don't create rocrate file when we skip the feature commit 709e67f Author: mirpedrol <[email protected]> Date: Mon Dec 16 11:46:35 2024 +0100 Remove Dumpler from ruamel yaml commit 0c4b0c0 Merge: 2b2b435 5ac5767 Author: Júlia Mir Pedrol <[email protected]> Date: Mon Dec 16 11:35:31 2024 +0100 Merge branch 'dev' into fix-pre-commit-template commit 2b2b435 Author: mirpedrol <[email protected]> Date: Mon Dec 16 11:34:30 2024 +0100 prettify template and printing .nf-core.yml commit 5ac5767 Merge: a8f63cd 76ac617 Author: Matthias Zepper <[email protected]> Date: Fri Dec 13 19:49:50 2024 +0100 Merge pull request #3351 from MatthiasZepper/no_env_in_download_action Replace Github environment usage in Download Action commit 76ac617 Author: Matthias Zepper <[email protected]> Date: Fri Dec 13 14:11:56 2024 +0100 Remove endraw statement that 'nf-core pipelines' create does not like. commit 1fbd011 Author: nf-core-bot <[email protected]> Date: Fri Dec 13 12:44:24 2024 +0000 [automated] Update CHANGELOG.md commit 9f61e85 Author: mirpedrol <[email protected]> Date: Fri Dec 13 13:30:05 2024 +0100 run pre-commit from a git repo commit f6159c9 Author: mirpedrol <[email protected]> Date: Fri Dec 13 13:29:17 2024 +0100 don't run prettier on ro-crate json file commit a8f63cd Merge: 6eaa998 4db108c Author: Sateesh_Peri <[email protected]> Date: Fri Dec 13 17:58:57 2024 +0530 Merge pull request #3357 from nf-core/usage-typo-fix Add missing p commit 059473c Author: mirpedrol <[email protected]> Date: Fri Dec 13 13:21:09 2024 +0100 fix pre-commit linting failures commit 4db108c Author: nf-core-bot <[email protected]> Date: Fri Dec 13 12:08:36 2024 +0000 [automated] Update CHANGELOG.md commit edd29e0 Author: James A. Fellows Yates <[email protected]> Date: Fri Dec 13 13:07:30 2024 +0100 Add missing p commit ac26924 Merge: f02d6bb 6eaa998 Author: Matthias Zepper <[email protected]> Date: Fri Dec 13 11:10:17 2024 +0100 Merge branch 'dev' into no_env_in_download_action commit 6eaa998 Merge: 06980d4 a2c2339 Author: Júlia Mir Pedrol <[email protected]> Date: Fri Dec 13 11:07:58 2024 +0100 Merge pull request #3356 from mirpedrol/fix-include-modules-config fix including modules.config commit f02d6bb Author: Júlia Mir Pedrol <[email protected]> Date: Thu Dec 12 11:14:52 2024 +0100 Update nf_core/pipeline-template/.github/workflows/awsfulltest.yml commit e32293d Author: mashehu <[email protected]> Date: Tue Dec 10 16:01:04 2024 +0100 update changelog commit 4c32e47 Author: mashehu <[email protected]> Date: Tue Dec 10 16:00:03 2024 +0100 fix if clause commit 4958cf0 Author: mashehu <[email protected]> Date: Tue Dec 10 15:40:28 2024 +0100 Be more verbose in approval check action commit a8065da Author: Matthias Hörtenhuber <[email protected]> Date: Thu Dec 12 10:59:54 2024 +0100 Revert "don't set up loggin level to error [no changelog]" commit 060eff5 Author: Matthias Zepper <[email protected]> Date: Fri Dec 13 10:58:08 2024 +0100 Apply suggestions from code review Co-authored-by: Matthias Hörtenhuber <[email protected]> commit a2c2339 Author: mirpedrol <[email protected]> Date: Fri Dec 13 10:47:18 2024 +0100 revert #3301 until we add linting from #2508 commit eed09ba Author: nf-core-bot <[email protected]> Date: Fri Dec 13 09:38:20 2024 +0000 [automated] Update CHANGELOG.md commit 4cf8607 Author: mirpedrol <[email protected]> Date: Fri Dec 13 10:36:28 2024 +0100 fix including modules.config commit 06980d4 Merge: aef5e16 8c5855f Author: Júlia Mir Pedrol <[email protected]> Date: Fri Dec 13 09:38:59 2024 +0100 Merge pull request #3354 from mashehu/fix-ro-crate-in-bump-version Fix ro crate in bump version commit 8c5855f Author: Júlia Mir Pedrol <[email protected]> Date: Fri Dec 13 08:19:50 2024 +0000 get max of 100 branch names commit b1ebca0 Merge: 307d0d4 aef5e16 Author: Júlia Mir Pedrol <[email protected]> Date: Fri Dec 13 08:53:30 2024 +0100 Merge branch 'dev' into fix-ro-crate-in-bump-version commit aef5e16 Merge: 3c20e00 d65da79 Author: Júlia Mir Pedrol <[email protected]> Date: Fri Dec 13 08:46:32 2024 +0100 Merge pull request #3353 from mashehu/bump-version-3_1_1dev bump version to 3.1.1dev commit 307d0d4 Author: mashehu <[email protected]> Date: Thu Dec 12 16:09:53 2024 +0100 only bump ro-crate if it already exists commit d65da79 Author: mashehu <[email protected]> Date: Thu Dec 12 15:04:39 2024 +0100 bump version to 3.1.1dev commit 62ebfc1 Author: Matthias Zepper <[email protected]> Date: Thu Dec 12 11:35:57 2024 +0100 Replace Github environment usage in Download Action. commit 3c20e00 Merge: f77737d c2a9dee Author: Júlia Mir Pedrol <[email protected]> Date: Thu Dec 12 11:30:04 2024 +0100 Merge pull request #3338 from mashehu/more-verbose-awsfulltest-checks Be more verbose in approval check action commit c2a9dee Author: Júlia Mir Pedrol <[email protected]> Date: Thu Dec 12 11:14:52 2024 +0100 Update nf_core/pipeline-template/.github/workflows/awsfulltest.yml commit f77737d Merge: d56b528 8f00659 Author: Matthias Hörtenhuber <[email protected]> Date: Thu Dec 12 11:12:01 2024 +0100 Merge pull request #3350 from nf-core/revert-3349-sync-debugging commit 8f00659 Author: Matthias Hörtenhuber <[email protected]> Date: Thu Dec 12 10:59:54 2024 +0100 Revert "don't set up loggin level to error [no changelog]" commit d56b528 Merge: 1af4c61 e92f327 Author: Júlia Mir Pedrol <[email protected]> Date: Thu Dec 12 10:21:37 2024 +0100 Merge pull request #3349 from mirpedrol/sync-debugging don't set up loggin level to error [no changelog] commit e92f327 Author: mirpedrol <[email protected]> Date: Thu Dec 12 10:00:43 2024 +0100 don't set up loggin level to error commit 1af4c61 Merge: 380be6c be38c15 Author: Matthias Hörtenhuber <[email protected]> Date: Thu Dec 12 09:24:47 2024 +0100 Merge pull request #3347 from mashehu/specify-ref-in-sync-yml commit be38c15 Author: mashehu <[email protected]> Date: Wed Dec 11 20:06:58 2024 +0100 use same ref in checkout as triggered the workflow commit 380be6c Author: mirpedrol <[email protected]> Date: Wed Dec 11 16:10:05 2024 +0100 cleanup debugging echo commit 3858e38 Author: mirpedrol <[email protected]> Date: Wed Dec 11 16:03:12 2024 +0100 try exiting pipeline directory before saving defaultBranch commit 1de1034 Author: mirpedrol <[email protected]> Date: Wed Dec 11 15:34:37 2024 +0100 echo message to sync GHA commit e8b6a9f Merge: a4965f3 df5b323 Author: Júlia Mir Pedrol <[email protected]> Date: Wed Dec 11 14:58:34 2024 +0100 Merge pull request #3345 from mirpedrol/sync-default-branch add more debugging on sync GHA [no changelog] commit df5b323 Author: mirpedrol <[email protected]> Date: Wed Dec 11 14:51:17 2024 +0100 add more debugging on sync GHA commit a4965f3 Merge: 06db03f 6148983 Author: Júlia Mir Pedrol <[email protected]> Date: Wed Dec 11 12:12:13 2024 +0100 Merge pull request #3342 from mirpedrol/sync-default-branch go back to original directory after configuring git defaultBranch [no changelog] commit 6148983 Author: mirpedrol <[email protected]> Date: Wed Dec 11 11:44:22 2024 +0100 go back to original directory after configuring git defaultBranch commit 06db03f Merge: 1a22106 379bad0 Author: Júlia Mir Pedrol <[email protected]> Date: Wed Dec 11 11:13:59 2024 +0100 Merge pull request #3339 from mashehu/add-verbose-mode-to-sync Add verbose mode to sync action commit 379bad0 Author: Júlia Mir Pedrol <[email protected]> Date: Wed Dec 11 10:03:37 2024 +0000 add input debug for workflow_dispatch sync action commit bb3a252 Author: Júlia Mir Pedrol <[email protected]> Date: Wed Dec 11 10:42:54 2024 +0100 Apply suggestions from code review commit 5c8937e Author: mashehu <[email protected]> Date: Tue Dec 10 17:19:32 2024 +0100 update changelog commit fa4e074 Author: mashehu <[email protected]> Date: Tue Dec 10 17:17:02 2024 +0100 add verbose mode to sync action commit 1748613 Author: mashehu <[email protected]> Date: Tue Dec 10 16:01:04 2024 +0100 update changelog commit f7ced6b Author: mashehu <[email protected]> Date: Tue Dec 10 16:00:03 2024 +0100 fix if clause commit 0b7fe50 Author: mashehu <[email protected]> Date: Tue Dec 10 15:40:28 2024 +0100 Be more verbose in approval check action commit 1a22106 Author: mashehu <[email protected]> Date: Tue Dec 10 15:17:06 2024 +0100 fix Changelog commit 15b044d Author: mashehu <[email protected]> Date: Tue Dec 10 15:15:26 2024 +0100 change working dir when setting defaultBranch commit 7a69b8c Merge: 666fc9f 0e7c870 Author: mashehu <[email protected]> Date: Tue Dec 10 14:44:40 2024 +0100 Merge branch 'dev' of github.com:nf-core/tools into fix-sync-grep commit 666fc9f Author: mashehu <[email protected]> Date: Tue Dec 10 14:44:12 2024 +0100 fix path for nextflow.config grep commit 0e7c870 Merge: a791707 5ee2d52 Author: Matthias Hörtenhuber <[email protected]> Date: Tue Dec 10 14:33:03 2024 +0100 Merge pull request #3337 from mashehu/fix-init-branch-in-sync-action set git defaultBranch to master in sync action commit 5ee2d52 Author: mashehu <[email protected]> Date: Tue Dec 10 14:30:14 2024 +0100 use nextflow.config to set defaultBranch commit 60ae1af Author: mashehu <[email protected]> Date: Tue Dec 10 13:26:07 2024 +0100 update changelog commit de00162 Author: mashehu <[email protected]> Date: Tue Dec 10 13:20:46 2024 +0100 set git defaultBranch to master in sync action commit a791707 Merge: 05e7b95 47054ad Author: Matthias Hörtenhuber <[email protected]> Date: Tue Dec 10 12:44:04 2024 +0100 Merge pull request #3335 from mashehu/set-default-branch-to-master set default_branch to master for now commit 47054ad Merge: 7110fff 05e7b95 Author: Matthias Hörtenhuber <[email protected]> Date: Tue Dec 10 12:25:27 2024 +0100 Merge branch 'dev' into set-default-branch-to-master commit 7110fff Author: mashehu <[email protected]> Date: Tue Dec 10 12:20:01 2024 +0100 update changelog commit e9cde59 Author: mashehu <[email protected]> Date: Tue Dec 10 12:17:54 2024 +0100 set default_branch to master for now commit 05e7b95 Merge: 55ca4d4 953055d Author: Matthias Hörtenhuber <[email protected]> Date: Tue Dec 10 11:38:06 2024 +0100 Merge pull request #3334 from mashehu/update-crate-with-version-bump rocrate: Update crate with version bump and handle new contributor field commit 953055d Author: mashehu <[email protected]> Date: Tue Dec 10 11:22:01 2024 +0100 fix type error commit 8a78d4b Author: Matthias Hörtenhuber <[email protected]> Date: Tue Dec 10 10:51:44 2024 +0100 Update nf_core/pipelines/rocrate.py commit b976ec3 Author: mashehu <[email protected]> Date: Tue Dec 10 10:16:12 2024 +0100 update changelog commit 6ae3de5 Author: mashehu <[email protected]> Date: Tue Dec 10 10:14:47 2024 +0100 handle new author field commit 3e81adb Author: mashehu <[email protected]> Date: Tue Dec 10 10:13:51 2024 +0100 update version in ro crate on version bump commit 55ca4d4 Merge: 5497cac 0e62e6e Author: Matthias Hörtenhuber <[email protected]> Date: Mon Dec 9 18:57:09 2024 +0100 Merge pull request #3333 from mashehu/fix-duplicated-ro-crate-entries commit 0e62e6e Author: mashehu <[email protected]> Date: Mon Dec 9 18:13:37 2024 +0100 update changelog commit 3c4fa81 Author: mashehu <[email protected]> Date: Mon Dec 9 18:12:08 2024 +0100 rocrate: remove duplicated entries for name and version commit 5497cac Merge: 4ea867a 045aaec Author: Júlia Mir Pedrol <[email protected]> Date: Mon Dec 9 17:30:06 2024 +0100 Merge pull request #3332 from mashehu/fix-gitpod-yml Don't break gitpod.yml with template string commit 045aaec Author: mashehu <[email protected]> Date: Mon Dec 9 17:11:04 2024 +0100 fix template string commit 5b1cf24 Author: Matthias Hörtenhuber <[email protected]> Date: Mon Dec 9 17:09:32 2024 +0100 Update nf_core/pipeline-template/.gitpod.yml Co-authored-by: Júlia Mir Pedrol <[email protected]> commit 15880be Author: mashehu <[email protected]> Date: Mon Dec 9 16:54:17 2024 +0100 make prettier happy commit 337143d Author: mashehu <[email protected]> Date: Mon Dec 9 16:43:57 2024 +0100 update changelog commit 5bc9952 Merge: 0385490 77ccc6a Author: mashehu <[email protected]> Date: Mon Dec 9 16:41:43 2024 +0100 Merge branch 'fix-gitpod-yml' of github.com:mashehu/tools into fix-gitpod-yml commit 0385490 Author: mashehu <[email protected]> Date: Mon Dec 9 16:41:31 2024 +0100 don't break gitpod.yml with template string commit 4ea867a Merge: 3f85556 8c9888b Author: Matthias Hörtenhuber <[email protected]> Date: Mon Dec 9 16:09:09 2024 +0100 Merge pull request #3330 from mashehu/skip-GRCh37 Template: Remove mention of GRCh37 if igenomes is skipped commit 3f85556 Merge: 7586248 a59e929 Author: Matthias Hörtenhuber <[email protected]> Date: Mon Dec 9 16:02:06 2024 +0100 Merge pull request #3331 from mirpedrol/revert-textual-dev-1.7.0 Revert textual dev 1.7.0 [no changelog] commit 8c9888b Merge: 1da1fc6 7586248 Author: mashehu <[email protected]> Date: Mon Dec 9 15:51:16 2024 +0100 Merge branch 'dev' of github.com:nf-core/tools into skip-GRCh37 # Conflicts: # nf_core/pipeline-template/.gitpod.yml commit a59e929 Author: mirpedrol <[email protected]> Date: Mon Dec 9 15:44:24 2024 +0100 revert updating textual-dev to 1.7.0 commit 1da1fc6 Author: mashehu <[email protected]> Date: Mon Dec 9 15:27:29 2024 +0100 update changelog commit e073622 Author: mashehu <[email protected]> Date: Mon Dec 9 15:23:56 2024 +0100 add missing closing tag commit 76ac145 Author: mashehu <[email protected]> Date: Mon Dec 9 15:23:20 2024 +0100 remove mention of GRCh37 from template if igenomes is skipped closes #3322 commit 7586248 Merge: edbeee3 afdb012 Author: Matthias Hörtenhuber <[email protected]> Date: Mon Dec 9 13:52:54 2024 +0100 Merge pull request #3329 from mashehu/bump-version-3_1_0 Bump version 3.1.0 commit afdb012 Author: Júlia Mir Pedrol <[email protected]> Date: Mon Dec 9 12:29:16 2024 +0000 add highlights and version updates sections to changelog commit ae1066c Author: mashehu <[email protected]> Date: Mon Dec 9 13:10:57 2024 +0100 bump to 3.1.0 commit edbeee3 Merge: 7e30b29 ee12866 Author: Júlia Mir Pedrol <[email protected]> Date: Mon Dec 9 12:58:26 2024 +0100 Merge pull request #3328 from mirpedrol/update-template-components Update template components commit 7e30b29 Merge: 99dba72 4ab2637 Author: Júlia Mir Pedrol <[email protected]> Date: Mon Dec 9 12:51:02 2024 +0100 Merge pull request #3308 from nf-core/renovate/textual-dev-1.x Update dependency textual-dev to v1.7.0 commit ee12866 Author: nf-core-bot <[email protected]> Date: Mon Dec 9 11:45:14 2024 +0000 [automated] Update CHANGELOG.md commit f209096 Author: mirpedrol <[email protected]> Date: Mon Dec 9 12:43:50 2024 +0100 fix jinja template missing endif commit 69f00bc Author: mirpedrol <[email protected]> Date: Mon Dec 9 12:40:42 2024 +0100 update utils_nfcore_pipeline swf commit 4ab2637 Merge: c5ffcf8 99dba72 Author: Júlia Mir Pedrol <[email protected]> Date: Mon Dec 9 12:34:23 2024 +0100 Merge branch 'dev' into renovate/textual-dev-1.x commit 99dba72 Merge: 98285e3 e5f0bd3 Author: Júlia Mir Pedrol <[email protected]> Date: Mon Dec 9 12:31:05 2024 +0100 Merge pull request #3292 from nf-core/vs-code-tests build: Setup VS Code tests commit e5f0bd3 Merge: a39ed59 98285e3 Author: Júlia Mir Pedrol <[email protected]> Date: Mon Dec 9 12:04:05 2024 +0100 Merge branch 'dev' into vs-code-tests commit 98285e3 Merge: 582774b 7a03d90 Author: Matthias Hörtenhuber <[email protected]> Date: Mon Dec 9 12:03:18 2024 +0100 Merge pull request #3323 from mashehu/fix-api-doc-headers fix headers in api docs commit 582774b Merge: b14b504 9f4036c Author: Júlia Mir Pedrol <[email protected]> Date: Mon Dec 9 12:03:04 2024 +0100 Merge pull request #3304 from nf-core/remove-channel-operations-from-oncomplete Remove toList() channel operation from inside onComplete block commit 9f4036c Merge: f22d7d9 b14b504 Author: Júlia Mir Pedrol <[email protected]> Date: Mon Dec 9 11:06:25 2024 +0100 Merge branch 'dev' into remove-channel-operations-from-oncomplete commit 7a03d90 Author: nf-core-bot <[email protected]> Date: Mon Dec 9 09:47:45 2024 +0000 [automated] Fix code linting commit efdced2 Merge: f54e123 b14b504 Author: Matthias Hörtenhuber <[email protected]> Date: Mon Dec 9 10:44:03 2024 +0100 Merge branch 'dev' into fix-api-doc-headers commit b14b504 Merge: 0450503 9c0f2ac Author: Phil Ewels <[email protected]> Date: Sat Dec 7 08:10:25 2024 +0100 Merge pull request #3326 from nf-core/modules-outside-nf-core-too commit 0450503 Merge: b2132cf cc38f8d Author: lmReef <[email protected]> Date: Sat Dec 7 10:47:24 2024 +1300 Merge pull request #3317 from lmReef/fix-linting-error Fix meta_yml linting error commit cc38f8d Merge: 3cc7646 b2132cf Author: lmReef <[email protected]> Date: Sat Dec 7 10:27:12 2024 +1300 Merge branch 'dev' into fix-linting-error commit b2132cf Merge: 0ba1c70 af05e4a Author: Matthias Hörtenhuber <[email protected]> Date: Fri Dec 6 22:24:03 2024 +0100 Merge pull request #3321 from lmReef/fix-module-section-regex commit af05e4a Merge: faded6a 0ba1c70 Author: lmReef <[email protected]> Date: Sat Dec 7 10:04:17 2024 +1300 Merge branch 'dev' into fix-module-section-regex commit 3cc7646 Merge: c5dc6ac 0ba1c70 Author: lmReef <[email protected]> Date: Sat Dec 7 10:04:15 2024 +1300 Merge branch 'dev' into fix-linting-error commit 9c0f2ac Merge: ba447fb 0ba1c70 Author: Phil Ewels <[email protected]> Date: Fri Dec 6 19:25:24 2024 +0100 Merge branch 'dev' into modules-outside-nf-core-too commit 0ba1c70 Author: nf-core-bot <[email protected]> Date: Fri Dec 6 13:55:42 2024 +0000 [automated] Update CHANGELOG.md commit 6a59a97 Author: Mahesh Binzer-Panchal <[email protected]> Date: Fri Dec 6 13:50:30 2024 +0000 Update gitpod vscode extensions to use nf-core extension pack commit ba447fb Author: nf-core-bot <[email protected]> Date: Thu Dec 5 22:57:35 2024 +0000 [automated] Update CHANGELOG.md commit da16adb Author: Phil Ewels <[email protected]> Date: Thu Dec 5 23:56:27 2024 +0100 Make prompt less nf-core specific commit c5dc6ac Merge: c3fd9bb 978f865 Author: lmReef <[email protected]> Date: Fri Dec 6 08:45:34 2024 +1300 Merge branch 'dev' into fix-linting-error commit faded6a Merge: c22c571 978f865 Author: lmReef <[email protected]> Date: Fri Dec 6 08:45:21 2024 +1300 Merge branch 'dev' into fix-module-section-regex commit 978f865 Merge: e8510cc c03f212 Author: Matthias Hörtenhuber <[email protected]> Date: Thu Dec 5 19:49:45 2024 +0100 Merge pull request #3325 from nf-core/renovate/astral-sh-ruff-pre-commit-0.x commit c03f212 Author: nf-core-bot <[email protected]> Date: Thu Dec 5 16:52:26 2024 +0000 [automated] Update CHANGELOG.md commit 2c5932e Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Date: Thu Dec 5 16:49:54 2024 +0000 Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.2 commit f54e123 Author: nf-core-bot <[email protected]> Date: Thu Dec 5 16:04:21 2024 +0000 [automated] Update CHANGELOG.md commit e8510cc Merge: f4b5b5d ce866c6 Author: Júlia Mir Pedrol <[email protected]> Date: Thu Dec 5 16:47:32 2024 +0100 Merge pull request #3142 from mashehu/master-to-main Allow `main` as default channel commit f4b5b5d Merge: a9d97e4 c23af55 Author: Matthias Hörtenhuber <[email protected]> Date: Thu Dec 5 16:36:36 2024 +0100 Merge pull request #3298 from nf-core/subworkflow-messages Improve subworkflow nf-test migration warning commit 6ddfe4d Author: mashehu <[email protected]> Date: Thu Dec 5 16:30:44 2024 +0100 fix headers commit c23af55 Author: nf-core-bot <[email protected]> Date: Thu Dec 5 15:19:54 2024 +0000 [automated] Update CHANGELOG.md commit a9d97e4 Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Date: Thu Dec 5 12:16:57 2024 +0000 Update python:3.12-slim Docker digest to 2b00791 (#3319) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> commit ce866c6 Author: Júlia Mir Pedrol <[email protected]> Date: Thu Dec 5 11:55:09 2024 +0100 Remove not needed setup-java step commit c22c571 Author: lmReef <[email protected]> Date: Thu Dec 5 10:14:01 2024 +1300 Revert "[automated] Update CHANGELOG.md" This reverts commit 355dff2. commit 9996df9 Author: lmReef <[email protected]> Date: Thu Dec 5 10:11:58 2024 +1300 update changelog commit 355dff2 Author: nf-core-bot <[email protected]> Date: Wed Dec 4 21:10:36 2024 +0000 [automated] Update CHANGELOG.md commit 57a92a0 Author: lmReef <[email protected]> Date: Thu Dec 5 09:34:08 2024 +1300 fix: module section linter regex commit c3fd9bb Author: lmReef <[email protected]> Date: Thu Dec 5 08:59:07 2024 +1300 fix: add explicit str type to self.process_name commit f22d7d9 Author: Rob Syme <[email protected]> Date: Wed Dec 4 08:09:57 2024 -0500 Revert changes to nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf commit b94435b Author: Júlia Mir Pedrol <[email protected]> Date: Wed Dec 4 09:48:13 2024 +0000 remove too many raw/endraw in branch.yml commit 4a8e976 Author: lmReef <[email protected]> Date: Wed Dec 4 10:41:19 2024 +1300 update changelog entry with link commit d3d9c72 Author: lmReef <[email protected]> Date: Wed Dec 4 10:29:10 2024 +1300 update changelog commit b04351d Author: lmReef <[email protected]> Date: Wed Dec 4 09:54:53 2024 +1300 fix: python linting warn commit dc9c3b1 Author: lmReef <[email protected]> Date: Wed Dec 4 09:43:11 2024 +1300 fix: linting error in meta_yml where module.process_name is always "" commit 229a232 Author: mashehu <[email protected]> Date: Tue Dec 3 18:14:33 2024 +0100 disambiguate in more places commit 2e4a8ed Author: mashehu <[email protected]> Date: Tue Dec 3 16:50:53 2024 +0100 use contect to figure out if it master or main Co-authored-by: @mirpredrol commit 9c43f15 Author: mashehu <[email protected]> Date: Tue Dec 3 15:36:20 2024 +0100 avoid confusion by separating the string commit 14480d2 Author: mashehu <[email protected]> Date: Tue Dec 3 15:26:31 2024 +0100 use java v17 commit 1857ebf Author: mashehu <[email protected]> Date: Tue Dec 3 14:46:55 2024 +0100 add missing setup-java action commit 8bc1a30 Author: mashehu <[email protected]> Date: Tue Dec 3 14:43:11 2024 +0100 nope, setup-java it is commit a604cb5 Author: mashehu <[email protected]> Date: Tue Dec 3 14:37:17 2024 +0100 set the variable manually commit 2475ad1 Merge: 4b2338f a7351a2 Author: Júlia Mir Pedrol <[email protected]> Date: Tue Dec 3 13:35:46 2024 +0000 Merge branch 'dev' of https://github.com/nf-core/tools into remove-channel-operations-from-oncomplete commit 4b2338f Author: Júlia Mir Pedrol <[email protected]> Date: Tue Dec 3 13:32:17 2024 +0000 update modules and subworkflows commit 00b8ae0 Author: mashehu <[email protected]> Date: Tue Dec 3 14:18:06 2024 +0100 pin java version 21 in CI commit e9ed94e Author: mashehu <[email protected]> Date: Tue Dec 3 14:08:04 2024 +0100 set defaultBranch in nextflow config to allow `main` commit 831548e Merge: 73957fd a7351a2 Author: Matthias Hörtenhuber <[email protected]> Date: Tue Dec 3 13:55:21 2024 +0100 Merge branch 'dev' into master-to-main commit 73957fd Merge: bd9608d 41b4516 Author: mashehu <[email protected]> Date: Tue Dec 3 13:54:11 2024 +0100 Merge branch 'main' of github.com:nf-core/tools into master-to-main # Conflicts: # .github/RELEASE_CHECKLIST.md # .github/workflows/branch.yml # .github/workflows/pytest.yml # nf_core/pipeline-template/README.md # nf_core/pipeline-template/assets/schema_input.json # nf_core/pipeline-template/nextflow_schema.json commit bd9608d Author: Matthias Hörtenhuber <[email protected]> Date: Tue Dec 3 13:38:33 2024 +0100 Update nf_core/components/create.py commit a39ed59 Merge: 35eb958 a7351a2 Author: Júlia Mir Pedrol <[email protected]> Date: Tue Dec 3 13:27:47 2024 +0100 Merge branch 'dev' into vs-code-tests commit abb0fa2 Author: Robert Syme <[email protected]> Date: Fri Nov 29 14:34:37 2024 -0500 Remove toList() channel operation from inside onComplete block This PR resolves an important bug in the nf-core template, whereby all workflows will hang if the --email parameter is supplied. The onComplete block will hang if there are any (queue) channel operations inside the block. All values in the onComplete block must be resolved to single values or value channels _before_ the onComplete block starts. The async channels are not available inside onComplete, so calling the toList() operation will hang forever as the async queue channel will never be completed. commit c5ffcf8 Author: nf-core-bot <[email protected]> Date: Sun Dec 1 02:09:38 2024 +0000 [automated] Update CHANGELOG.md commit 456aa05 Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Date: Sun Dec 1 02:08:49 2024 +0000 Update dependency textual-dev to v1.7.0 commit 35eb958 Author: Edmund Miller <[email protected]> Date: Tue Nov 26 02:17:48 2024 +0000 Add Python terminal env settings commit 805620b Author: Edmund Miller <[email protected]> Date: Mon Nov 25 11:09:22 2024 -0600 fix(#3297): Update warning message for pytest-workflow commit 3456346 Author: nf-core-bot <[email protected]> Date: Thu Nov 21 17:29:49 2024 +0000 [automated] Update CHANGELOG.md commit dd477ab Author: Edmund Miller <[email protected]> Date: Wed Nov 20 22:50:15 2024 -0600 build: Setup VS Code tests commit fa2750a Author: mashehu <[email protected]> Date: Tue Aug 27 15:18:27 2024 +0200 use format instead of f-string commit 19ec188 Author: mashehu <[email protected]> Date: Tue Aug 27 10:30:07 2024 +0200 revert to format commit 2054550 Author: mashehu <[email protected]> Date: Tue Aug 27 10:07:47 2024 +0200 fix quotes commit 9d2a3ab Author: mashehu <[email protected]> Date: Tue Aug 27 09:12:38 2024 +0200 fix order in lint commit ed0fb1b Author: mashehu <[email protected]> Date: Tue Aug 27 09:08:51 2024 +0200 set default value for default branch commit da91519 Author: mashehu <[email protected]> Date: Tue Aug 27 09:00:05 2024 +0200 fix schema check commit 5b3dabd Author: mashehu <[email protected]> Date: Tue Aug 27 08:47:44 2024 +0200 fix order of initialization commit 889e59e Author: mashehu <[email protected]> Date: Tue Aug 27 08:41:53 2024 +0200 handle missing self.default_branch commit 6fc6da2 Author: mashehu <[email protected]> Date: Tue Aug 27 07:30:15 2024 +0200 change pipeline template and tooling to allow `main` as default branch commit 77ccc6a Author: mashehu <[email protected]> Date: Wed Dec 20 15:51:04 2023 +0100 set gitpod.yml docker image to latest
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continuing in #3083 :) |
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I had to open a new PR since I was not able to push to the original branch in #3083
This updates the branch by merging
devand fixing merge conflicts