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Dev -> Master for 2.13 #2781

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merged 241 commits into from
Feb 20, 2024
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8d45289
fix conflicts between editor config and prettier
mashehu Jan 30, 2024
ad20579
remove trailing whitespace in template
mashehu Jan 30, 2024
0c9e01a
automatically rerun actions on github instead of self-hosted
mashehu Jan 30, 2024
61508da
remove ignored option
mashehu Jan 30, 2024
2f7b371
run test_components always on self-hosted runners
mashehu Jan 30, 2024
5ab5597
add comment explaining runner logic
mashehu Jan 30, 2024
e47c05b
run sync setup locally to start quicker
mashehu Jan 30, 2024
b029dea
bump to 2.13dev
mirpedrol Feb 1, 2024
a622eb1
Merge pull request #2721 from mirpedrol/bump-2.13dev
mirpedrol Feb 1, 2024
5966957
fix ignoring changes in partial template files
mashehu Feb 1, 2024
cffda64
[automated] Update CHANGELOG.md
nf-core-bot Feb 1, 2024
a651445
fix changelog
mashehu Feb 1, 2024
9e219eb
fix one more path
mashehu Feb 1, 2024
32d3488
update ruff for dev tools [skip changelog]
mashehu Feb 2, 2024
08e44f3
update ruff in template and add it to pre-commit step
mashehu Feb 2, 2024
c75959f
[automated] Update CHANGELOG.md
nf-core-bot Feb 2, 2024
06f4e7d
Merge pull request #2724 from mashehu/update-ruff
mashehu Feb 2, 2024
9447625
fix docstring
mashehu Feb 2, 2024
f189835
Update nf_core/pipeline-template/.pre-commit-config.yaml
mashehu Feb 2, 2024
900b0ff
Merge branch 'dev' into update-ruff-template
mashehu Feb 2, 2024
59808f2
Update codecov/codecov-action digest to e0b68c6
renovate[bot] Feb 1, 2024
aabbb35
[automated] Update CHANGELOG.md
nf-core-bot Feb 3, 2024
fe25da0
Update README.md
maxulysse Feb 5, 2024
b2ee77d
[automated] Update CHANGELOG.md
nf-core-bot Feb 5, 2024
28a2f24
fix changelog
mashehu Feb 5, 2024
02eba1d
Merge pull request #2729 from nf-core/maxulysse-patch-4
maxulysse Feb 5, 2024
157860c
Pin dependencies
renovate[bot] Feb 6, 2024
bf7d0b5
Update pre-commit hook astral-sh/ruff-pre-commit to v0.2.1
renovate[bot] Feb 6, 2024
7e3ecc5
[automated] Update CHANGELOG.md
nf-core-bot Feb 6, 2024
4a060da
Merge branch 'dev' of github.com:nf-core/tools into dev
mashehu Feb 6, 2024
b2f7c48
make creat-lint-wf composable
mashehu Feb 6, 2024
0fe8896
[automated] Update CHANGELOG.md
nf-core-bot Feb 6, 2024
eec8293
move to correct folder
mashehu Feb 6, 2024
a446895
Merge branch 'dev' of https://github.com/nf-core/tools into update-ru…
mashehu Feb 6, 2024
bf82578
fix composite action syntax
mashehu Feb 6, 2024
650538d
Merge branch 'convert-create-lint-wf-action' of github.com:mashehu/to…
mashehu Feb 6, 2024
23316a3
fix action syntax
mashehu Feb 6, 2024
c965539
clean up actions
mashehu Feb 6, 2024
03b044a
Merge pull request #2725 from mashehu/update-ruff-template
mashehu Feb 6, 2024
1b6e214
add step with bump to release version
mashehu Feb 6, 2024
979883a
Merge pull request #2720 from nf-core/renovate/pin-dependencies
mashehu Feb 6, 2024
f3f7abc
Download CI Test: Set dev as the default branch and add customisation…
MatthiasZepper Feb 2, 2024
de73d39
Update Changelog.
MatthiasZepper Feb 2, 2024
90dd793
fix trailing whitespace
mashehu Feb 6, 2024
3bc83a5
Merge pull request #2727 from MatthiasZepper/download_test_branch_fix
mashehu Feb 6, 2024
31b1db7
Merge pull request #2730 from nf-core/renovate/astral-sh-ruff-pre-com…
mashehu Feb 6, 2024
c2f95ef
Place checkouts in try block and force if needed
gregorysprenger Feb 6, 2024
ebdfff0
[automated] Update CHANGELOG.md
nf-core-bot Feb 6, 2024
23a3000
Merge 'dev' into branch force_checkout
gregorysprenger Feb 6, 2024
0b1903a
Merge branch 'dev' into fix-editorconfig
mashehu Feb 7, 2024
7899cd5
Merge pull request #2706 from mashehu/fix-editorconfig
mashehu Feb 7, 2024
21c2c12
Merge branch 'dev' into fix-files-unchanged-parital
mashehu Feb 7, 2024
fca9d74
Merge pull request #2722 from mashehu/fix-files-unchanged-parital
mashehu Feb 7, 2024
47713a2
only use force on specific git errors
mashehu Feb 7, 2024
5e73945
Merge branch 'dev' into force_checkout
mashehu Feb 7, 2024
5163e4a
add logic to second occurrence of commands
mashehu Feb 7, 2024
7d97824
Merge branch 'force_checkout' of github.com:gregorysprenger/tools int…
mashehu Feb 7, 2024
372a9f2
fix tests
mashehu Feb 7, 2024
3e95d02
[automated] Update CHANGELOG.md
nf-core-bot Feb 7, 2024
c161ebb
Update python:3.11-slim Docker digest to 2a746e2
renovate[bot] Feb 8, 2024
56b1dd1
Merge branch 'dev' of github.com:nf-core/tools into dev
mashehu Feb 8, 2024
5ed48a9
Install utils_subworkflows_* from nf-core/modules
drpatelh Feb 8, 2024
f6572df
add regular component update action
mashehu Feb 8, 2024
a9c73f1
Merge branch 'dev' into convert-create-lint-wf-action
mashehu Feb 8, 2024
2768222
[automated] Fix code linting
nf-core-bot Feb 8, 2024
a1417c0
add test nf-core commands only in the tools repo
mirpedrol Feb 8, 2024
53487ec
Remove lib directory from pipeline template
drpatelh Feb 8, 2024
fdd020d
fix syntax
mashehu Feb 8, 2024
99fb69f
Change output channel name in input_check subworkflow
drpatelh Feb 8, 2024
bae90f0
Delete custom/dumpsoftwareversions module
drpatelh Feb 8, 2024
a78d41b
Delete fasta from test.config
drpatelh Feb 8, 2024
7343ce4
Add local subworkflow for pipeline utilities
drpatelh Feb 8, 2024
3f86b93
one more
mashehu Feb 8, 2024
090a395
Update main workflows in pipeline to use utils_* subworkflows
drpatelh Feb 8, 2024
7a1e4bc
debug workflow
mashehu Feb 8, 2024
a0fe759
add shell
mashehu Feb 8, 2024
b7e6935
remove clean up action
mashehu Feb 8, 2024
31f7eb3
Apply suggestions from code review
mashehu Feb 8, 2024
d934d75
Merge pull request #2733 from mashehu/convert-create-lint-wf-action
mashehu Feb 8, 2024
4124943
Update actions/setup-python action to v5
renovate[bot] Feb 8, 2024
7b4720a
[automated] Update CHANGELOG.md
nf-core-bot Feb 8, 2024
b6c3965
only paths or paths-ignore is allowed
mashehu Feb 8, 2024
fdf3e54
Disable native version detection in MultiQC
drpatelh Feb 8, 2024
ffcc42d
Merge pull request #2739 from nf-core/renovate/actions-setup-python-5.x
mashehu Feb 8, 2024
63e67fc
fix jinja rendering of download_pipeline.yml
mirpedrol Feb 8, 2024
a8f5274
Update actions/checkout action to v4
renovate[bot] Feb 8, 2024
fb20ba7
Merge pull request #2738 from nf-core/renovate/actions-checkout-4.x
mashehu Feb 8, 2024
1ad52e4
Pin dependencies
renovate[bot] Feb 8, 2024
9cdccd1
Merge pull request #2737 from nf-core/renovate/pin-dependencies
mashehu Feb 8, 2024
a5f8f4e
Merge pull request #2742 from mirpedrol/jinja-fix
MatthiasZepper Feb 8, 2024
5214976
Add checkProfileProvided function back in
drpatelh Feb 8, 2024
a52503b
[automated] Update CHANGELOG.md
nf-core-bot Feb 9, 2024
3d9e14e
Merge branch 'dev' into renovate/python-3.11-slim
mashehu Feb 9, 2024
f8fb333
Merge pull request #2743 from nf-core/renovate/python-3.11-slim
mashehu Feb 9, 2024
d646ae6
linting: add looser comparison when linting pipeline logos
mashehu Feb 9, 2024
8ca34cb
[automated] Update CHANGELOG.md
nf-core-bot Feb 9, 2024
f312397
Merge pull request #2740 from mashehu/fix-ci-error
mashehu Feb 9, 2024
1d9839e
Merge branch 'dev' into make-filecmp-less-strict
mashehu Feb 9, 2024
201562c
Update nf-core/setup-nextflow digest to b9f764e
renovate[bot] Feb 9, 2024
7832a44
update utils_nfcore_pipeline in the template
mirpedrol Feb 9, 2024
91b1529
add multiqc report to completion email
mirpedrol Feb 10, 2024
d7610a1
Merge pull request #2744 from mashehu/make-filecmp-less-strict
mashehu Feb 12, 2024
48c7026
add methodsDescriptionText to multiqc report
mirpedrol Feb 12, 2024
650cb30
Merge branch 'dev' of github.com:nf-core/tools into force_checkout
mashehu Feb 12, 2024
bbf3fac
update template subworkflows
mirpedrol Feb 12, 2024
125cc59
remove warn exceeding resources
mirpedrol Feb 12, 2024
c64ed82
fix SimpleTemplateEngine error by writing to the file
mirpedrol Feb 12, 2024
77aa1cb
check if we are in a modules repo before we force checkout
mashehu Feb 13, 2024
aa2c14c
Merge pull request #2734 from gregorysprenger/force_checkout
mashehu Feb 13, 2024
e56999f
use nf-validation to create input channel
mirpedrol Feb 13, 2024
75f833f
linting: warn if groovy files in lib exist
mirpedrol Feb 13, 2024
a62c307
fix pytests
mirpedrol Feb 13, 2024
0dd064a
rename local subworkflow from the template
mirpedrol Feb 13, 2024
5b5b30a
fix editorconfig errors in the template
mirpedrol Feb 13, 2024
4b51a27
chore(deps): update gitpod/workspace-base docker digest to 45e7617
renovate[bot] Feb 12, 2024
17ffafb
[automated] Update CHANGELOG.md
nf-core-bot Feb 13, 2024
71a0eec
rename local subworkflow with jinja
mirpedrol Feb 14, 2024
ff69ee3
fix more pytests
mirpedrol Feb 14, 2024
b325944
fix creating a template without igenomes
mirpedrol Feb 14, 2024
3bd4cfe
return multiqc description as string
mirpedrol Feb 14, 2024
f6375dd
fix docstrings
mashehu Feb 14, 2024
cf62ce0
fix more docstrings
mashehu Feb 14, 2024
a558126
Merge pull request #2750 from mashehu/fix-docstrings
mashehu Feb 14, 2024
9c89874
fix prettier inconsistencies in the pipeline template
mirpedrol Feb 14, 2024
7f7e920
fix more linting tests
mirpedrol Feb 14, 2024
5b8dca6
Update python:3.11-slim Docker digest to ce81dc5
renovate[bot] Feb 14, 2024
068e24a
add working generate-api-doc.sh script
mashehu Feb 15, 2024
28c0196
apply suggestions from code review
mirpedrol Feb 15, 2024
8b61207
optimize script
mashehu Feb 15, 2024
bba8f93
Add fix for disk space issues on github actions runners
apeltzer Feb 15, 2024
e351460
[automated] Update CHANGELOG.md
nf-core-bot Feb 15, 2024
b20c734
Apply suggestions from code review
ewels Feb 15, 2024
23bd8da
[automated] Update CHANGELOG.md
nf-core-bot Feb 15, 2024
e283676
Update README.md
RaqManzano Feb 15, 2024
54f836d
Remove duplicate changelog entry
ewels Feb 15, 2024
b1c1410
Update CHANGELOG.md
mashehu Feb 15, 2024
4d2ed49
Merge pull request #2755 from nf-core/fix-gha-runners
apeltzer Feb 15, 2024
4149598
chore(deps): pin jlumbroso/free-disk-space action to 54081f1
renovate[bot] Feb 15, 2024
a69512f
[automated] Update CHANGELOG.md
nf-core-bot Feb 15, 2024
60eecb7
Merge branch 'dev' into RaqManzano-patch-1
ewels Feb 15, 2024
d214ed6
Fix badge links
ewels Feb 15, 2024
a32f6d3
[automated] Update CHANGELOG.md
nf-core-bot Feb 15, 2024
f8ce923
Merge pull request #2756 from nf-core/renovate/pin-dependencies
mashehu Feb 15, 2024
1a57b3a
fix changelog
mashehu Feb 15, 2024
59214f5
merge api docs actions to one and trigger action on website repo
mashehu Feb 15, 2024
018ce82
add missing remark script
mashehu Feb 15, 2024
3ef8990
[automated] Update CHANGELOG.md
nf-core-bot Feb 15, 2024
5543bc4
add outdir option to generate script
mashehu Feb 15, 2024
baef8a0
fix index pages
mashehu Feb 15, 2024
7350e32
update path for remark script
mashehu Feb 15, 2024
e275dff
don't update members in api docs
mashehu Feb 15, 2024
3711b74
remove typo
mashehu Feb 15, 2024
4186bcb
just copy files over and then go back to current branch
mashehu Feb 15, 2024
808dc68
fix for lower level emphasis terms
mashehu Feb 15, 2024
afa0cf0
add debugging
mashehu Feb 15, 2024
c0b6e19
handle emphasis before the rest
mashehu Feb 15, 2024
8f40d4a
remove debugging
mashehu Feb 15, 2024
0f33118
convert the whole heading to code
mashehu Feb 15, 2024
714a1aa
tidy up remark code
mashehu Feb 15, 2024
5dd018d
fix one more index page
mashehu Feb 15, 2024
fac45e7
use different remark logic
mashehu Feb 15, 2024
eb8d992
Merge branch 'switch-to-md-api-docs' of github.com:mashehu/tools into…
mashehu Feb 15, 2024
2c11e4b
fix api index page
mashehu Feb 16, 2024
2224747
Merge pull request #2757 from RaqManzano/RaqManzano-patch-1
mashehu Feb 16, 2024
f016e45
Merge pull request #2736 from nf-core/rm_lib
mirpedrol Feb 16, 2024
c393ed4
template: add hashtags to release announcement on mastodon
mashehu Feb 16, 2024
8011af4
[automated] Update CHANGELOG.md
nf-core-bot Feb 16, 2024
49cf4f0
Merge branch 'dev' into add-hashtags
mashehu Feb 16, 2024
c1f06ea
Apply suggestions from code review
mashehu Feb 16, 2024
d9f8443
add profile parameter to nf-test command
mashehu Feb 16, 2024
997d274
handle multiple module imports in linting
mashehu Feb 16, 2024
27da6a6
[automated] Update CHANGELOG.md
nf-core-bot Feb 16, 2024
243ec64
fix changelog
mashehu Feb 16, 2024
2dd530e
Merge pull request #2761 from mashehu/add-hashtags
mashehu Feb 16, 2024
a840790
fix tests
mashehu Feb 16, 2024
1d04268
add prompt for extra files
mashehu Feb 16, 2024
364a836
Merge pull request #2758 from mashehu/switch-to-md-api-docs
mashehu Feb 16, 2024
1fa125d
chore(deps): update actions/github-script action to v7
renovate[bot] Feb 16, 2024
74e6ad7
[automated] Update CHANGELOG.md
nf-core-bot Feb 16, 2024
03a0226
Merge branch 'dev' into fix-lint-multiple-module-import
mashehu Feb 16, 2024
bb7e638
[automated] Update CHANGELOG.md
nf-core-bot Feb 16, 2024
fba4272
fix tests
mashehu Feb 16, 2024
58b6712
Merge branch 'nf-test-profiles' of github.com:mashehu/tools into nf-t…
mashehu Feb 16, 2024
6a7980d
fix all occurences
mashehu Feb 16, 2024
75f6f19
remove options
mashehu Feb 16, 2024
31dc437
simplify logic and add tests
mashehu Feb 16, 2024
c2dcb12
Merge pull request #2766 from nf-core/renovate/actions-github-script-7.x
mashehu Feb 17, 2024
edc1e26
chore(deps): update dawidd6/action-download-artifact digest to f6b0bac
renovate[bot] Feb 15, 2024
9bbf4cd
chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.2.2
renovate[bot] Feb 18, 2024
df9b5e2
[automated] Update CHANGELOG.md
nf-core-bot Feb 18, 2024
83fa6ba
Merge pull request #2769 from nf-core/renovate/astral-sh-ruff-pre-com…
mashehu Feb 18, 2024
1baba7c
handle symlink when migrating pytest
mirpedrol Feb 18, 2024
ea614e1
[automated] Update CHANGELOG.md
nf-core-bot Feb 18, 2024
3e1ca3d
patch: handle file not found when it is an added file to a module
mirpedrol Feb 18, 2024
30b3d51
[automated] Update CHANGELOG.md
nf-core-bot Feb 18, 2024
a61549e
add test for symlink deletion
mashehu Feb 19, 2024
d9bb78a
Update CHANGELOG.md
mashehu Feb 19, 2024
6cff41c
fix github action syntax, remove now unneeded makefile [skip changelog]
mashehu Feb 19, 2024
7dcdd2f
fix action name
mashehu Feb 19, 2024
f4a4c2f
no need for a prompt if it profile is set as a parameter
mashehu Feb 19, 2024
706de8f
Merge pull request #2767 from mashehu/nf-test-profiles
mashehu Feb 19, 2024
105270f
Merge pull request #2772 from mashehu/fix-api-build-request
mashehu Feb 19, 2024
0193225
Merge pull request #2762 from mashehu/fix-lint-multiple-module-import
mashehu Feb 19, 2024
c3a3dae
add missing comma
mashehu Feb 19, 2024
263d47f
Merge pull request #2773 from mashehu/fix-api-build-request
mashehu Feb 19, 2024
8f94653
move all possible config files during update
mashehu Feb 19, 2024
6b65a01
fix test name
mashehu Feb 19, 2024
b0da4ff
Merge branch 'dev' into migrate-pytest-symlink
mashehu Feb 19, 2024
a47369a
Merge pull request #2763 from mashehu/keep-nf-config-files-on-compone…
mashehu Feb 19, 2024
eeca1b2
fix generate api docs script, gsed-> sed
mashehu Feb 19, 2024
69b0a69
Merge branch 'dev' into extra-module-file
mirpedrol Feb 19, 2024
7d6a2a5
Merge pull request #2775 from mashehu/fix-build-script
mashehu Feb 19, 2024
cc99981
Merge pull request #2770 from mirpedrol/migrate-pytest-symlink
mirpedrol Feb 19, 2024
a24a733
Merge branch 'dev' into extra-module-file
mashehu Feb 19, 2024
fa9ca91
Merge pull request #2771 from mirpedrol/extra-module-file
mirpedrol Feb 19, 2024
2240168
update modules in template
mashehu Feb 19, 2024
9f56fcb
[automated] Update CHANGELOG.md
nf-core-bot Feb 19, 2024
2e076d1
move also subdirectories during update
mashehu Feb 19, 2024
f12aec5
bring back lost files
mashehu Feb 19, 2024
87633c1
Merge branch 'update-template-modules' of github.com:mashehu/tools in…
mashehu Feb 19, 2024
749b2ce
fix changelog
mashehu Feb 19, 2024
2d380c5
bump version to dev -> 2.13
mashehu Feb 19, 2024
e070ebb
add code review suggestions
mashehu Feb 20, 2024
656b0f8
update pyproject toml according to ruff 0.2.0
mashehu Feb 20, 2024
69e3ece
format pyproject.toml file
mashehu Feb 20, 2024
9951f25
update pipeline template pyproject.toml according to ruff 0.2.0
mirpedrol Feb 20, 2024
e00e528
Merge pull request #2779 from mashehu/fix-ruff-setting
mashehu Feb 20, 2024
89a3154
add full path of nextflow.config to update files
mirpedrol Feb 20, 2024
faee542
Update CHANGELOG.md
mashehu Feb 20, 2024
eae4cca
Merge pull request #2776 from mashehu/update-template-modules
mashehu Feb 20, 2024
ae5971d
Merge pull request #2777 from mashehu/fix-missing-files-in-update
mashehu Feb 20, 2024
d95729e
Update CHANGELOG.md
mashehu Feb 20, 2024
8352dc1
update gitpod image to latest
mirpedrol Feb 20, 2024
fdda81d
chore(deps): update gitpod/workspace-base docker digest to 728e1fa
renovate[bot] Feb 19, 2024
04ff0f2
[automated] Update CHANGELOG.md
nf-core-bot Feb 20, 2024
189d23a
Merge pull request #2778 from mashehu/bump-version-2_13
mashehu Feb 20, 2024
8525502
Generate new screengrabs with rich-codex
github-actions[bot] Feb 20, 2024
275a902
increase timeout for sfw update screenshot
mashehu Feb 20, 2024
b3fd496
Merge pull request #2782 from mashehu/fix-rich-codex
mashehu Feb 20, 2024
6a6562a
Generate new screengrabs with rich-codex
github-actions[bot] Feb 20, 2024
f4871ef
update changelog
mirpedrol Feb 20, 2024
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[automated] Update CHANGELOG.md
  • Loading branch information
nf-core-bot committed Feb 6, 2024
commit 7e3ecc56765b3a1641943871cda9cb118405f211
1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
### General

- Update codecov/codecov-action digest to e0b68c6 ([#2728](https://github.com/nf-core/tools/pull/2728))
- Update pre-commit hook astral-sh/ruff-pre-commit to v0.2.1 ([#2730](https://github.com/nf-core/tools/pull/2730))

## [v2.12.1 - Aluminium Wolf - Patch](https://github.com/nf-core/tools/releases/tag/2.12.1) - [2024-02-01]

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