Update template components #3328
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mashehu
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Dec 9, 2024
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commit 769f8dd Merge: 5ac5767 d44bcdf Author: Júlia Mir Pedrol <mirp.julia@gmail.com> Date: Mon Dec 16 14:23:39 2024 +0100 Merge pull request nf-core#3358 from mirpedrol/fix-pre-commit-template Fix pre commit template commit d44bcdf Author: mirpedrol <mirp.julia@gmail.com> Date: Mon Dec 16 13:06:36 2024 +0100 more prettier fixes commit 2c78c5e Author: mirpedrol <mirp.julia@gmail.com> Date: Mon Dec 16 12:28:59 2024 +0100 more template prittier fixing commit d19e3e0 Author: mirpedrol <mirp.julia@gmail.com> 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 <mirp.julia@gmail.com> Date: Mon Dec 16 12:08:20 2024 +0100 fix more prettier modifications form the template commit ac703bf Author: mirpedrol <mirp.julia@gmail.com> Date: Mon Dec 16 11:58:43 2024 +0100 don't create rocrate file when we skip the feature commit 709e67f Author: mirpedrol <mirp.julia@gmail.com> Date: Mon Dec 16 11:46:35 2024 +0100 Remove Dumpler from ruamel yaml commit 0c4b0c0 Merge: 2b2b435 5ac5767 Author: Júlia Mir Pedrol <mirp.julia@gmail.com> Date: Mon Dec 16 11:35:31 2024 +0100 Merge branch 'dev' into fix-pre-commit-template commit 2b2b435 Author: mirpedrol <mirp.julia@gmail.com> Date: Mon Dec 16 11:34:30 2024 +0100 prettify template and printing .nf-core.yml commit 5ac5767 Merge: a8f63cd 76ac617 Author: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com> Date: Fri Dec 13 19:49:50 2024 +0100 Merge pull request nf-core#3351 from MatthiasZepper/no_env_in_download_action Replace Github environment usage in Download Action commit 76ac617 Author: Matthias Zepper <MatthiasZepper@users.noreply.github.com> 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 <core@nf-co.re> Date: Fri Dec 13 12:44:24 2024 +0000 [automated] Update CHANGELOG.md commit 9f61e85 Author: mirpedrol <mirp.julia@gmail.com> Date: Fri Dec 13 13:30:05 2024 +0100 run pre-commit from a git repo commit f6159c9 Author: mirpedrol <mirp.julia@gmail.com> 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 <33637490+sateeshperi@users.noreply.github.com> Date: Fri Dec 13 17:58:57 2024 +0530 Merge pull request nf-core#3357 from nf-core/usage-typo-fix Add missing p commit 059473c Author: mirpedrol <mirp.julia@gmail.com> Date: Fri Dec 13 13:21:09 2024 +0100 fix pre-commit linting failures commit 4db108c Author: nf-core-bot <core@nf-co.re> Date: Fri Dec 13 12:08:36 2024 +0000 [automated] Update CHANGELOG.md commit edd29e0 Author: James A. Fellows Yates <jfy133@gmail.com> Date: Fri Dec 13 13:07:30 2024 +0100 Add missing p commit ac26924 Merge: f02d6bb 6eaa998 Author: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com> 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 <mirp.julia@gmail.com> Date: Fri Dec 13 11:07:58 2024 +0100 Merge pull request nf-core#3356 from mirpedrol/fix-include-modules-config fix including modules.config commit f02d6bb Author: Júlia Mir Pedrol <mirp.julia@gmail.com> Date: Thu Dec 12 11:14:52 2024 +0100 Update nf_core/pipeline-template/.github/workflows/awsfulltest.yml commit e32293d Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 10 16:01:04 2024 +0100 update changelog commit 4c32e47 Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 10 16:00:03 2024 +0100 fix if clause commit 4958cf0 Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 10 15:40:28 2024 +0100 Be more verbose in approval check action commit a8065da Author: Matthias Hörtenhuber <mashehu@users.noreply.github.com> 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 <6963520+MatthiasZepper@users.noreply.github.com> Date: Fri Dec 13 10:58:08 2024 +0100 Apply suggestions from code review Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> commit a2c2339 Author: mirpedrol <mirp.julia@gmail.com> Date: Fri Dec 13 10:47:18 2024 +0100 revert nf-core#3301 until we add linting from nf-core#2508 commit eed09ba Author: nf-core-bot <core@nf-co.re> Date: Fri Dec 13 09:38:20 2024 +0000 [automated] Update CHANGELOG.md commit 4cf8607 Author: mirpedrol <mirp.julia@gmail.com> Date: Fri Dec 13 10:36:28 2024 +0100 fix including modules.config commit 06980d4 Merge: aef5e16 8c5855f Author: Júlia Mir Pedrol <mirp.julia@gmail.com> Date: Fri Dec 13 09:38:59 2024 +0100 Merge pull request nf-core#3354 from mashehu/fix-ro-crate-in-bump-version Fix ro crate in bump version commit 8c5855f Author: Júlia Mir Pedrol <mirp.julia@gmail.com> Date: Fri Dec 13 08:19:50 2024 +0000 get max of 100 branch names commit b1ebca0 Merge: 307d0d4 aef5e16 Author: Júlia Mir Pedrol <mirp.julia@gmail.com> 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 <mirp.julia@gmail.com> Date: Fri Dec 13 08:46:32 2024 +0100 Merge pull request nf-core#3353 from mashehu/bump-version-3_1_1dev bump version to 3.1.1dev commit 307d0d4 Author: mashehu <mashehu3@gmail.com> Date: Thu Dec 12 16:09:53 2024 +0100 only bump ro-crate if it already exists commit d65da79 Author: mashehu <mashehu3@gmail.com> Date: Thu Dec 12 15:04:39 2024 +0100 bump version to 3.1.1dev commit 62ebfc1 Author: Matthias Zepper <MatthiasZepper@users.noreply.github.com> 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 <mirp.julia@gmail.com> Date: Thu Dec 12 11:30:04 2024 +0100 Merge pull request nf-core#3338 from mashehu/more-verbose-awsfulltest-checks Be more verbose in approval check action commit c2a9dee Author: Júlia Mir Pedrol <mirp.julia@gmail.com> 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 <mashehu@users.noreply.github.com> Date: Thu Dec 12 11:12:01 2024 +0100 Merge pull request nf-core#3350 from nf-core/revert-3349-sync-debugging commit 8f00659 Author: Matthias Hörtenhuber <mashehu@users.noreply.github.com> 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 <mirp.julia@gmail.com> Date: Thu Dec 12 10:21:37 2024 +0100 Merge pull request nf-core#3349 from mirpedrol/sync-debugging don't set up loggin level to error [no changelog] commit e92f327 Author: mirpedrol <mirp.julia@gmail.com> 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 <mashehu@users.noreply.github.com> Date: Thu Dec 12 09:24:47 2024 +0100 Merge pull request nf-core#3347 from mashehu/specify-ref-in-sync-yml commit be38c15 Author: mashehu <mashehu3@gmail.com> Date: Wed Dec 11 20:06:58 2024 +0100 use same ref in checkout as triggered the workflow commit 380be6c Author: mirpedrol <mirp.julia@gmail.com> Date: Wed Dec 11 16:10:05 2024 +0100 cleanup debugging echo commit 3858e38 Author: mirpedrol <mirp.julia@gmail.com> Date: Wed Dec 11 16:03:12 2024 +0100 try exiting pipeline directory before saving defaultBranch commit 1de1034 Author: mirpedrol <mirp.julia@gmail.com> Date: Wed Dec 11 15:34:37 2024 +0100 echo message to sync GHA commit e8b6a9f Merge: a4965f3 df5b323 Author: Júlia Mir Pedrol <mirp.julia@gmail.com> Date: Wed Dec 11 14:58:34 2024 +0100 Merge pull request nf-core#3345 from mirpedrol/sync-default-branch add more debugging on sync GHA [no changelog] commit df5b323 Author: mirpedrol <mirp.julia@gmail.com> Date: Wed Dec 11 14:51:17 2024 +0100 add more debugging on sync GHA commit a4965f3 Merge: 06db03f 6148983 Author: Júlia Mir Pedrol <mirp.julia@gmail.com> Date: Wed Dec 11 12:12:13 2024 +0100 Merge pull request nf-core#3342 from mirpedrol/sync-default-branch go back to original directory after configuring git defaultBranch [no changelog] commit 6148983 Author: mirpedrol <mirp.julia@gmail.com> 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 <mirp.julia@gmail.com> Date: Wed Dec 11 11:13:59 2024 +0100 Merge pull request nf-core#3339 from mashehu/add-verbose-mode-to-sync Add verbose mode to sync action commit 379bad0 Author: Júlia Mir Pedrol <mirp.julia@gmail.com> Date: Wed Dec 11 10:03:37 2024 +0000 add input debug for workflow_dispatch sync action commit bb3a252 Author: Júlia Mir Pedrol <mirp.julia@gmail.com> Date: Wed Dec 11 10:42:54 2024 +0100 Apply suggestions from code review commit 5c8937e Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 10 17:19:32 2024 +0100 update changelog commit fa4e074 Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 10 17:17:02 2024 +0100 add verbose mode to sync action commit 1748613 Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 10 16:01:04 2024 +0100 update changelog commit f7ced6b Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 10 16:00:03 2024 +0100 fix if clause commit 0b7fe50 Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 10 15:40:28 2024 +0100 Be more verbose in approval check action commit 1a22106 Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 10 15:17:06 2024 +0100 fix Changelog commit 15b044d Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 10 15:15:26 2024 +0100 change working dir when setting defaultBranch commit 7a69b8c Merge: 666fc9f 0e7c870 Author: mashehu <mashehu3@gmail.com> 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 <mashehu3@gmail.com> Date: Tue Dec 10 14:44:12 2024 +0100 fix path for nextflow.config grep commit 0e7c870 Merge: a791707 5ee2d52 Author: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Date: Tue Dec 10 14:33:03 2024 +0100 Merge pull request nf-core#3337 from mashehu/fix-init-branch-in-sync-action set git defaultBranch to master in sync action commit 5ee2d52 Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 10 14:30:14 2024 +0100 use nextflow.config to set defaultBranch commit 60ae1af Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 10 13:26:07 2024 +0100 update changelog commit de00162 Author: mashehu <mashehu3@gmail.com> 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 <mashehu@users.noreply.github.com> Date: Tue Dec 10 12:44:04 2024 +0100 Merge pull request nf-core#3335 from mashehu/set-default-branch-to-master set default_branch to master for now commit 47054ad Merge: 7110fff 05e7b95 Author: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Date: Tue Dec 10 12:25:27 2024 +0100 Merge branch 'dev' into set-default-branch-to-master commit 7110fff Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 10 12:20:01 2024 +0100 update changelog commit e9cde59 Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 10 12:17:54 2024 +0100 set default_branch to master for now commit 05e7b95 Merge: 55ca4d4 953055d Author: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Date: Tue Dec 10 11:38:06 2024 +0100 Merge pull request nf-core#3334 from mashehu/update-crate-with-version-bump rocrate: Update crate with version bump and handle new contributor field commit 953055d Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 10 11:22:01 2024 +0100 fix type error commit 8a78d4b Author: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Date: Tue Dec 10 10:51:44 2024 +0100 Update nf_core/pipelines/rocrate.py commit b976ec3 Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 10 10:16:12 2024 +0100 update changelog commit 6ae3de5 Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 10 10:14:47 2024 +0100 handle new author field commit 3e81adb Author: mashehu <mashehu3@gmail.com> 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 <mashehu@users.noreply.github.com> Date: Mon Dec 9 18:57:09 2024 +0100 Merge pull request nf-core#3333 from mashehu/fix-duplicated-ro-crate-entries commit 0e62e6e Author: mashehu <mashehu3@gmail.com> Date: Mon Dec 9 18:13:37 2024 +0100 update changelog commit 3c4fa81 Author: mashehu <mashehu3@gmail.com> 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 <mirp.julia@gmail.com> Date: Mon Dec 9 17:30:06 2024 +0100 Merge pull request nf-core#3332 from mashehu/fix-gitpod-yml Don't break gitpod.yml with template string commit 045aaec Author: mashehu <mashehu3@gmail.com> Date: Mon Dec 9 17:11:04 2024 +0100 fix template string commit 5b1cf24 Author: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Date: Mon Dec 9 17:09:32 2024 +0100 Update nf_core/pipeline-template/.gitpod.yml Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com> commit 15880be Author: mashehu <mashehu3@gmail.com> Date: Mon Dec 9 16:54:17 2024 +0100 make prettier happy commit 337143d Author: mashehu <mashehu3@gmail.com> Date: Mon Dec 9 16:43:57 2024 +0100 update changelog commit 5bc9952 Merge: 0385490 77ccc6a Author: mashehu <mashehu3@gmail.com> 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 <mashehu3@gmail.com> 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 <mashehu@users.noreply.github.com> Date: Mon Dec 9 16:09:09 2024 +0100 Merge pull request nf-core#3330 from mashehu/skip-GRCh37 Template: Remove mention of GRCh37 if igenomes is skipped commit 3f85556 Merge: 7586248 a59e929 Author: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Date: Mon Dec 9 16:02:06 2024 +0100 Merge pull request nf-core#3331 from mirpedrol/revert-textual-dev-1.7.0 Revert textual dev 1.7.0 [no changelog] commit 8c9888b Merge: 1da1fc6 7586248 Author: mashehu <mashehu3@gmail.com> 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 <mirp.julia@gmail.com> Date: Mon Dec 9 15:44:24 2024 +0100 revert updating textual-dev to 1.7.0 commit 1da1fc6 Author: mashehu <mashehu3@gmail.com> Date: Mon Dec 9 15:27:29 2024 +0100 update changelog commit e073622 Author: mashehu <mashehu3@gmail.com> Date: Mon Dec 9 15:23:56 2024 +0100 add missing closing tag commit 76ac145 Author: mashehu <mashehu3@gmail.com> Date: Mon Dec 9 15:23:20 2024 +0100 remove mention of GRCh37 from template if igenomes is skipped closes nf-core#3322 commit 7586248 Merge: edbeee3 afdb012 Author: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Date: Mon Dec 9 13:52:54 2024 +0100 Merge pull request nf-core#3329 from mashehu/bump-version-3_1_0 Bump version 3.1.0 commit afdb012 Author: Júlia Mir Pedrol <mirp.julia@gmail.com> Date: Mon Dec 9 12:29:16 2024 +0000 add highlights and version updates sections to changelog commit ae1066c Author: mashehu <mashehu3@gmail.com> Date: Mon Dec 9 13:10:57 2024 +0100 bump to 3.1.0 commit edbeee3 Merge: 7e30b29 ee12866 Author: Júlia Mir Pedrol <mirp.julia@gmail.com> Date: Mon Dec 9 12:58:26 2024 +0100 Merge pull request nf-core#3328 from mirpedrol/update-template-components Update template components commit 7e30b29 Merge: 99dba72 4ab2637 Author: Júlia Mir Pedrol <mirp.julia@gmail.com> Date: Mon Dec 9 12:51:02 2024 +0100 Merge pull request nf-core#3308 from nf-core/renovate/textual-dev-1.x Update dependency textual-dev to v1.7.0 commit ee12866 Author: nf-core-bot <core@nf-co.re> Date: Mon Dec 9 11:45:14 2024 +0000 [automated] Update CHANGELOG.md commit f209096 Author: mirpedrol <mirp.julia@gmail.com> Date: Mon Dec 9 12:43:50 2024 +0100 fix jinja template missing endif commit 69f00bc Author: mirpedrol <mirp.julia@gmail.com> Date: Mon Dec 9 12:40:42 2024 +0100 update utils_nfcore_pipeline swf commit 4ab2637 Merge: c5ffcf8 99dba72 Author: Júlia Mir Pedrol <mirp.julia@gmail.com> 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 <mirp.julia@gmail.com> Date: Mon Dec 9 12:31:05 2024 +0100 Merge pull request nf-core#3292 from nf-core/vs-code-tests build: Setup VS Code tests commit e5f0bd3 Merge: a39ed59 98285e3 Author: Júlia Mir Pedrol <mirp.julia@gmail.com> Date: Mon Dec 9 12:04:05 2024 +0100 Merge branch 'dev' into vs-code-tests commit 98285e3 Merge: 582774b 7a03d90 Author: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Date: Mon Dec 9 12:03:18 2024 +0100 Merge pull request nf-core#3323 from mashehu/fix-api-doc-headers fix headers in api docs commit 582774b Merge: b14b504 9f4036c Author: Júlia Mir Pedrol <mirp.julia@gmail.com> Date: Mon Dec 9 12:03:04 2024 +0100 Merge pull request nf-core#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 <mirp.julia@gmail.com> Date: Mon Dec 9 11:06:25 2024 +0100 Merge branch 'dev' into remove-channel-operations-from-oncomplete commit 7a03d90 Author: nf-core-bot <core@nf-co.re> Date: Mon Dec 9 09:47:45 2024 +0000 [automated] Fix code linting commit efdced2 Merge: f54e123 b14b504 Author: Matthias Hörtenhuber <mashehu@users.noreply.github.com> 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 <phil.ewels@seqera.io> Date: Sat Dec 7 08:10:25 2024 +0100 Merge pull request nf-core#3326 from nf-core/modules-outside-nf-core-too commit 0450503 Merge: b2132cf cc38f8d Author: lmReef <60915116+lmReef@users.noreply.github.com> Date: Sat Dec 7 10:47:24 2024 +1300 Merge pull request nf-core#3317 from lmReef/fix-linting-error Fix meta_yml linting error commit cc38f8d Merge: 3cc7646 b2132cf Author: lmReef <60915116+lmReef@users.noreply.github.com> Date: Sat Dec 7 10:27:12 2024 +1300 Merge branch 'dev' into fix-linting-error commit b2132cf Merge: 0ba1c70 af05e4a Author: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Date: Fri Dec 6 22:24:03 2024 +0100 Merge pull request nf-core#3321 from lmReef/fix-module-section-regex commit af05e4a Merge: faded6a 0ba1c70 Author: lmReef <60915116+lmReef@users.noreply.github.com> Date: Sat Dec 7 10:04:17 2024 +1300 Merge branch 'dev' into fix-module-section-regex commit 3cc7646 Merge: c5dc6ac 0ba1c70 Author: lmReef <60915116+lmReef@users.noreply.github.com> Date: Sat Dec 7 10:04:15 2024 +1300 Merge branch 'dev' into fix-linting-error commit 9c0f2ac Merge: ba447fb 0ba1c70 Author: Phil Ewels <phil.ewels@seqera.io> Date: Fri Dec 6 19:25:24 2024 +0100 Merge branch 'dev' into modules-outside-nf-core-too commit 0ba1c70 Author: nf-core-bot <core@nf-co.re> Date: Fri Dec 6 13:55:42 2024 +0000 [automated] Update CHANGELOG.md commit 6a59a97 Author: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> 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 <core@nf-co.re> Date: Thu Dec 5 22:57:35 2024 +0000 [automated] Update CHANGELOG.md commit da16adb Author: Phil Ewels <phil.ewels@seqera.io> Date: Thu Dec 5 23:56:27 2024 +0100 Make prompt less nf-core specific commit c5dc6ac Merge: c3fd9bb 978f865 Author: lmReef <60915116+lmReef@users.noreply.github.com> Date: Fri Dec 6 08:45:34 2024 +1300 Merge branch 'dev' into fix-linting-error commit faded6a Merge: c22c571 978f865 Author: lmReef <60915116+lmReef@users.noreply.github.com> 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 <mashehu@users.noreply.github.com> Date: Thu Dec 5 19:49:45 2024 +0100 Merge pull request nf-core#3325 from nf-core/renovate/astral-sh-ruff-pre-commit-0.x commit c03f212 Author: nf-core-bot <core@nf-co.re> 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 <core@nf-co.re> Date: Thu Dec 5 16:04:21 2024 +0000 [automated] Update CHANGELOG.md commit e8510cc Merge: f4b5b5d ce866c6 Author: Júlia Mir Pedrol <mirp.julia@gmail.com> Date: Thu Dec 5 16:47:32 2024 +0100 Merge pull request nf-core#3142 from mashehu/master-to-main Allow `main` as default channel commit f4b5b5d Merge: a9d97e4 c23af55 Author: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Date: Thu Dec 5 16:36:36 2024 +0100 Merge pull request nf-core#3298 from nf-core/subworkflow-messages Improve subworkflow nf-test migration warning commit 6ddfe4d Author: mashehu <mashehu3@gmail.com> Date: Thu Dec 5 16:30:44 2024 +0100 fix headers commit c23af55 Author: nf-core-bot <core@nf-co.re> 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 (nf-core#3319) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> commit ce866c6 Author: Júlia Mir Pedrol <mirp.julia@gmail.com> Date: Thu Dec 5 11:55:09 2024 +0100 Remove not needed setup-java step commit c22c571 Author: lmReef <ReefMatson@gmail.com> Date: Thu Dec 5 10:14:01 2024 +1300 Revert "[automated] Update CHANGELOG.md" This reverts commit 355dff2. commit 9996df9 Author: lmReef <ReefMatson@gmail.com> Date: Thu Dec 5 10:11:58 2024 +1300 update changelog commit 355dff2 Author: nf-core-bot <core@nf-co.re> Date: Wed Dec 4 21:10:36 2024 +0000 [automated] Update CHANGELOG.md commit 57a92a0 Author: lmReef <ReefMatson@gmail.com> Date: Thu Dec 5 09:34:08 2024 +1300 fix: module section linter regex commit c3fd9bb Author: lmReef <ReefMatson@gmail.com> Date: Thu Dec 5 08:59:07 2024 +1300 fix: add explicit str type to self.process_name commit f22d7d9 Author: Rob Syme <rob.syme@gmail.com> 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 <mirp.julia@gmail.com> Date: Wed Dec 4 09:48:13 2024 +0000 remove too many raw/endraw in branch.yml commit 4a8e976 Author: lmReef <ReefMatson@gmail.com> Date: Wed Dec 4 10:41:19 2024 +1300 update changelog entry with link commit d3d9c72 Author: lmReef <ReefMatson@gmail.com> Date: Wed Dec 4 10:29:10 2024 +1300 update changelog commit b04351d Author: lmReef <ReefMatson@gmail.com> Date: Wed Dec 4 09:54:53 2024 +1300 fix: python linting warn commit dc9c3b1 Author: lmReef <ReefMatson@gmail.com> 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 <mashehu3@gmail.com> Date: Tue Dec 3 18:14:33 2024 +0100 disambiguate in more places commit 2e4a8ed Author: mashehu <mashehu3@gmail.com> 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 <mashehu3@gmail.com> Date: Tue Dec 3 15:36:20 2024 +0100 avoid confusion by separating the string commit 14480d2 Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 3 15:26:31 2024 +0100 use java v17 commit 1857ebf Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 3 14:46:55 2024 +0100 add missing setup-java action commit 8bc1a30 Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 3 14:43:11 2024 +0100 nope, setup-java it is commit a604cb5 Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 3 14:37:17 2024 +0100 set the variable manually commit 2475ad1 Merge: 4b2338f a7351a2 Author: Júlia Mir Pedrol <mirp.julia@gmail.com> 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 <mirp.julia@gmail.com> Date: Tue Dec 3 13:32:17 2024 +0000 update modules and subworkflows commit 00b8ae0 Author: mashehu <mashehu3@gmail.com> Date: Tue Dec 3 14:18:06 2024 +0100 pin java version 21 in CI commit e9ed94e Author: mashehu <mashehu3@gmail.com> 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 <mashehu@users.noreply.github.com> Date: Tue Dec 3 13:55:21 2024 +0100 Merge branch 'dev' into master-to-main commit 73957fd Merge: bd9608d 41b4516 Author: mashehu <mashehu3@gmail.com> 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 <mashehu@users.noreply.github.com> Date: Tue Dec 3 13:38:33 2024 +0100 Update nf_core/components/create.py commit a39ed59 Merge: 35eb958 a7351a2 Author: Júlia Mir Pedrol <mirp.julia@gmail.com> Date: Tue Dec 3 13:27:47 2024 +0100 Merge branch 'dev' into vs-code-tests commit abb0fa2 Author: Robert Syme <rob.syme@gmail.com> 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 <core@nf-co.re> 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 <edmund.a.miller@gmail.com> Date: Tue Nov 26 02:17:48 2024 +0000 Add Python terminal env settings commit 805620b Author: Edmund Miller <git@edmundmiller.dev> Date: Mon Nov 25 11:09:22 2024 -0600 fix(nf-core#3297): Update warning message for pytest-workflow commit 3456346 Author: nf-core-bot <core@nf-co.re> Date: Thu Nov 21 17:29:49 2024 +0000 [automated] Update CHANGELOG.md commit dd477ab Author: Edmund Miller <git@edmundmiller.dev> Date: Wed Nov 20 22:50:15 2024 -0600 build: Setup VS Code tests commit fa2750a Author: mashehu <mashehu3@gmail.com> Date: Tue Aug 27 15:18:27 2024 +0200 use format instead of f-string commit 19ec188 Author: mashehu <mashehu3@gmail.com> Date: Tue Aug 27 10:30:07 2024 +0200 revert to format commit 2054550 Author: mashehu <mashehu3@gmail.com> Date: Tue Aug 27 10:07:47 2024 +0200 fix quotes commit 9d2a3ab Author: mashehu <mashehu3@gmail.com> Date: Tue Aug 27 09:12:38 2024 +0200 fix order in lint commit ed0fb1b Author: mashehu <mashehu3@gmail.com> Date: Tue Aug 27 09:08:51 2024 +0200 set default value for default branch commit da91519 Author: mashehu <mashehu3@gmail.com> Date: Tue Aug 27 09:00:05 2024 +0200 fix schema check commit 5b3dabd Author: mashehu <mashehu3@gmail.com> Date: Tue Aug 27 08:47:44 2024 +0200 fix order of initialization commit 889e59e Author: mashehu <mashehu3@gmail.com> Date: Tue Aug 27 08:41:53 2024 +0200 handle missing self.default_branch commit 6fc6da2 Author: mashehu <mashehu3@gmail.com> Date: Tue Aug 27 07:30:15 2024 +0200 change pipeline template and tooling to allow `main` as default branch commit 77ccc6a Author: mashehu <mashehu3@gmail.com> Date: Wed Dec 20 15:51:04 2023 +0100 set gitpod.yml docker image to latest
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