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Fix module section linter regex #3321

Merged
merged 6 commits into from
Dec 6, 2024
Merged

Fix module section linter regex #3321

merged 6 commits into from
Dec 6, 2024

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lmReef
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@lmReef lmReef commented Dec 4, 2024

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated

Description

Fix an issue where the regexs used to find where each section starts in the modules linter aren't robust enough and end up matching the wrong things.

Example

add something like container 'test_typescript:3.0.0' to a module and you'll see these tests fail because the regex r"script\s*:" matches script: in test_typescript:

image

@lmReef lmReef marked this pull request as ready for review December 4, 2024 21:15
@mashehu mashehu enabled auto-merge December 6, 2024 21:21
@mashehu mashehu merged commit b2132cf into nf-core:dev Dec 6, 2024
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codecov bot commented Dec 6, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 76.05%. Comparing base (c03f212) to head (af05e4a).
Report is 10 commits behind head on dev.

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jvfe added a commit to sanger-tol/nf-core-tools that referenced this pull request Dec 16, 2024
@jvfe
Squashed commit of the following:
fd98f95 
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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@lmReef @mashehu @nf-core-bot