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feat: Add Claude Code hooks for automated testing and linting #3774

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bbb041a
fixes to template logic
nvnieuwk Sep 2, 2025
9029471
bump nextflow to 25.04.0
nvnieuwk Sep 2, 2025
e9e5cdb
also bump CI nextflow version
nvnieuwk Sep 2, 2025
ec86cf3
Apply suggestions from code review
nvnieuwk Sep 2, 2025
0c803f8
prevent summary log duplication
nvnieuwk Sep 2, 2025
b172dec
Merge branch 'bump/nf-schema-2.5.0' of github.com:nvnieuwk/tools into…
nvnieuwk Sep 2, 2025
78b790e
Merge pull request #3569 from JulianFlesch/issues/3466-gitpod
JulianFlesch Sep 3, 2025
0cb2928
impr: Add hostRequirements to run with 4CPUs and 16GB ram by default …
JulianFlesch Sep 5, 2025
4f71d25
[automated] Update CHANGELOG.md
nf-core-bot Sep 5, 2025
b49cb9d
do not check pytest_modules.yml file, deprecating
mirpedrol Sep 8, 2025
3638a42
[automated] Update CHANGELOG.md
nf-core-bot Sep 8, 2025
5c707a0
update changelog
mirpedrol Sep 8, 2025
c3dd970
Merge pull request #3748 from mirpedrol/no-modules-pytest
mirpedrol Sep 8, 2025
10bb2c4
Fix: temporary files not moved and cleaned up correctly after singula…
JulianFlesch Sep 8, 2025
6d2705b
[automated] Update CHANGELOG.md
nf-core-bot Sep 8, 2025
7ae6720
Merge pull request #3746 from JulianFlesch/impr/devcontainer-resources
JulianFlesch Sep 8, 2025
caa53b5
Merging dev changes
JulianFlesch Sep 8, 2025
210d4ee
fix: Set 755 file permisson for image files after http download
JulianFlesch Sep 8, 2025
1f1c346
fix: change permission string from hexa to octal. Use temp file name
JulianFlesch Sep 8, 2025
5ec33a0
Merge pull request #3749 from JulianFlesch/issues/3742-download
JulianFlesch Sep 9, 2025
6d424b3
impr: run nextflow inspect in tempdir
JulianFlesch Sep 9, 2025
89e628d
impr: Add contextmanager for changing into temp direcotry and handlin…
JulianFlesch Sep 9, 2025
46787e9
Merge branch 'dev' into issues/3729-download-cleanup
JulianFlesch Sep 9, 2025
403fc2c
Add changes
JulianFlesch Sep 9, 2025
47724bb
Add check for docker daemon by running docker info
JulianFlesch Sep 9, 2025
51d285f
Add error handling around setup code.
JulianFlesch Sep 9, 2025
5d42968
bump nf-schema to 2.5.1
nvnieuwk Sep 10, 2025
43e06f1
Merge branch 'dev' into bump/nf-schema-2.5.0
nvnieuwk Sep 10, 2025
2e8795b
fix more issues
nvnieuwk Sep 10, 2025
5c7db2e
update linting to new nf-schema help message
nvnieuwk Sep 10, 2025
73e6ce5
bump nextflow version in readme
nvnieuwk Sep 10, 2025
75d5439
use aws anonymous client when using the default igenomes base
nvnieuwk Sep 10, 2025
a46fc2d
add previous fix to an if statement
nvnieuwk Sep 10, 2025
b60730b
bump missing nextflow versions
nvnieuwk Sep 10, 2025
9150467
fix a config mistake
nvnieuwk Sep 10, 2025
0e3b0f0
fix lint issues
nvnieuwk Sep 10, 2025
26b7b10
Merge pull request #3743 from nvnieuwk/bump/nf-schema-2.5.0
nvnieuwk Sep 10, 2025
10a4f43
"False" can never be returned
muffato Sep 12, 2025
5ded0a6
There is no such subworkflow_patch
muffato Sep 12, 2025
dd14e01
[automated] Update CHANGELOG.md
nf-core-bot Sep 13, 2025
604fa54
Updated the CHANGELOG
muffato Sep 13, 2025
f6fa9d5
Added linting tests for patched subworkflows
muffato Sep 13, 2025
d03a357
Another way of breaking the diff file
muffato Sep 13, 2025
8479e03
Update hook_url to use environment variable
matthdsm Sep 15, 2025
ad26187
Merge branch 'dev' into matthdsm-patch-1
matthdsm Sep 15, 2025
8d6e6da
[automated] Update CHANGELOG.md
nf-core-bot Sep 15, 2025
27e1315
Update usage.md charliecloud url
nschan Sep 16, 2025
1cff32b
fix(component_differ): fix the repeated printing of component diffs t…
awgymer Sep 17, 2025
4bd1c78
[automated] Update CHANGELOG.md
nf-core-bot Sep 17, 2025
202b471
Merge branch 'dev' into nschan-patch-1
nschan Sep 17, 2025
1c6b8cc
fix(template): update template CI conda installation to explicitly se…
prototaxites Sep 18, 2025
456841f
[automated] Update CHANGELOG.md
nf-core-bot Sep 18, 2025
b980cda
docs: update changelog
prototaxites Sep 18, 2025
31b79df
Merge pull request #3764 from prototaxites/conda_ci_fix
prototaxites Sep 18, 2025
6e09394
Merge branch 'dev' into nschan-patch-1
mashehu Sep 22, 2025
7207334
[automated] Update CHANGELOG.md
nf-core-bot Sep 22, 2025
c5e77bc
[automated] Update CHANGELOG.md
nf-core-bot Sep 22, 2025
f58c564
Merge pull request #3757 from nf-core/nschan-patch-1
mashehu Sep 22, 2025
7869345
update multiqc to 1.31
jpfeuffer Sep 22, 2025
ed92ea2
[automated] Update CHANGELOG.md
nf-core-bot Sep 22, 2025
c14850a
[automated] Update CHANGELOG.md
nf-core-bot Sep 22, 2025
c518ee6
Merge branch 'dev' into update/mqc1.31
mashehu Sep 22, 2025
a590391
[automated] Update Textual snapshots
nf-core-bot Sep 22, 2025
984398c
Use the org from the .nf-core.yml when linting manifest name and home…
rrahn Sep 23, 2025
369d2f1
[automated] Update CHANGELOG.md
nf-core-bot Sep 23, 2025
9fad021
Fix: Add NXF_VERSION environment variable to nf-test workflow
SZhengP Sep 23, 2025
b1ccfe9
[automated] Update CHANGELOG.md
nf-core-bot Sep 24, 2025
4164503
Merge pull request #3767 from rrahn/feature/dynamic-org-for-linting
SZhengP Sep 24, 2025
7d92154
resolve snaps manually
jpfeuffer Sep 25, 2025
9ebe70f
Add .nf-test/ to prettier ignore list
Joon-Klaps Sep 26, 2025
591ee86
[automated] Update CHANGELOG.md
nf-core-bot Sep 26, 2025
abf4c30
Merge pull request #3776 from nf-core/Joon-Klaps-patch-1
Joon-Klaps Sep 26, 2025
1ddf9ce
fix: Address PR review feedback
edmundmiller Sep 27, 2025
442eafe
Merge branch 'dev' into logo
mashehu Sep 29, 2025
f86712a
Merge branch 'dev' into fix/add-nxf-version-env
mashehu Sep 29, 2025
2ed2320
[automated] Update CHANGELOG.md
nf-core-bot Sep 29, 2025
a9bd678
Merge pull request #3770 from nf-core/fix/add-nxf-version-env
SZhengP Sep 29, 2025
71e507f
Merge branch 'dev' into matthdsm-patch-1
mashehu Sep 29, 2025
50d89c0
[automated] Update CHANGELOG.md
nf-core-bot Sep 29, 2025
b682f79
unittest.TestCase already provides setUp() to manage the setup phase
muffato Sep 30, 2025
7ba3e5e
Merge pull request #3755 from nf-core/subworkflow_patch
muffato Sep 30, 2025
65326c7
update nf-test to 0.9.3
mashehu Sep 30, 2025
cda5f65
[automated] Update CHANGELOG.md
nf-core-bot Sep 30, 2025
d59bce0
run `nf-core modules update multiqc`
mashehu Sep 30, 2025
bef9642
update error message
mashehu Sep 30, 2025
e06d775
update error messages
mashehu Sep 30, 2025
f66029f
Update dependency prompt_toolkit to <=3.0.52
renovate[bot] Oct 1, 2025
3e779f7
Update dependency textual to v5.3.0
renovate[bot] Oct 1, 2025
2ece3d6
[automated] Update CHANGELOG.md
nf-core-bot Oct 1, 2025
22176d7
[automated] Update CHANGELOG.md
nf-core-bot Oct 1, 2025
fa17a78
Merge pull request #3781 from mashehu/update-nf-test-to-0.9.3
mashehu Oct 1, 2025
b1e401c
Merge branch 'dev' into update/mqc1.31
mashehu Oct 1, 2025
dbff16a
Merge branch 'dev' into renovate/textual-5.x
mashehu Oct 1, 2025
b17fcd3
Merge branch 'dev' into renovate/prompt_toolkit-3.x
mashehu Oct 1, 2025
5361ed3
update modules.json
mashehu Oct 1, 2025
030fc2b
Merge pull request #3785 from nf-core/renovate/textual-5.x
mirpedrol Oct 1, 2025
f4ef362
Merge branch 'dev' into update-mastodon-announcement
mashehu Oct 1, 2025
2e6407b
Merge pull request #3741 from jfy133/update-mastodon-announcement
mashehu Oct 1, 2025
6e5bcae
update rich-click to 1.9
mashehu Oct 1, 2025
d9034aa
add subcommand aliases
mashehu Oct 1, 2025
4475032
Merge pull request #3715 from nf-core/logo
mirpedrol Oct 1, 2025
a3a5eac
set theme
mashehu Oct 1, 2025
62ce829
switch to new panel API
mashehu Oct 1, 2025
776616e
add singular form of subcommands as aliases
mashehu Oct 1, 2025
c027cc3
[automated] Update CHANGELOG.md
nf-core-bot Oct 1, 2025
bc88811
update release checklist to battle test pipeline template more
mirpedrol Oct 1, 2025
7891d8e
[automated] Update CHANGELOG.md
nf-core-bot Oct 1, 2025
bf57750
Merge branch 'dev' into matthdsm-patch-1
mashehu Oct 1, 2025
01ac55e
Merge pull request #3756 from nf-core/matthdsm-patch-1
mashehu Oct 1, 2025
f40f311
use default theme to get more distinguished alias colors
mashehu Oct 2, 2025
809bb65
Merge branch 'update-to-rich-click-0_9' of github.com:mashehu/tools i…
mashehu Oct 2, 2025
b3bc0f6
use same order for command alias and option short name
mashehu Oct 2, 2025
669edb2
Merge pull request #3788 from mirpedrol/update-release-checklist
mirpedrol Oct 2, 2025
fd80960
Merge pull request #3787 from mashehu/update-to-rich-click-0_9
mashehu Oct 2, 2025
d2508dc
Update python:3.13-slim Docker digest to 3a6ead7 (#3786)
renovate[bot] Oct 2, 2025
5de59e9
Merge branch 'dev' into renovate/prompt_toolkit-3.x
mashehu Oct 2, 2025
21350df
Update codecov/codecov-action digest to fdcc847 (#3717)
renovate[bot] Oct 2, 2025
558c22e
Merge branch 'dev' into renovate/migrate-config
mashehu Oct 2, 2025
7329b44
Merge pull request #3726 from nf-core/renovate/migrate-config
mashehu Oct 2, 2025
c41aba9
Merge pull request #3783 from nf-core/renovate/prompt_toolkit-3.x
mashehu Oct 2, 2025
095a4d0
Update pre-commit hook pre-commit/mirrors-mypy to v1.18.2
renovate[bot] Oct 2, 2025
77b7e70
Update dependency textual to v6
renovate[bot] Oct 2, 2025
a180b96
[automated] Update CHANGELOG.md
nf-core-bot Oct 2, 2025
ed14af6
[automated] Update CHANGELOG.md
nf-core-bot Oct 2, 2025
fc2a0d6
Update GitHub Actions (#3795)
renovate[bot] Oct 2, 2025
512ade2
Update python:3.13-slim Docker digest to 5f55cdf (#3796)
renovate[bot] Oct 2, 2025
3c2bab4
Merge branch 'dev' into renovate/pre-commit-mirrors-mypy-1.x
mashehu Oct 2, 2025
4da54fa
Merge pull request #3792 from nf-core/renovate/pre-commit-mirrors-myp…
mashehu Oct 2, 2025
4787544
Update pre-commit hook pre-commit/pre-commit-hooks to v6
renovate[bot] Oct 3, 2025
e047d84
[automated] Update CHANGELOG.md
nf-core-bot Oct 3, 2025
4afdaba
Update pre-commit hook astral-sh/ruff-pre-commit to v0.13.3
renovate[bot] Oct 3, 2025
d7214cb
[automated] Update CHANGELOG.md
nf-core-bot Oct 3, 2025
eef5586
Merge pull request #3797 from nf-core/renovate/pre-commit-pre-commit-…
mashehu Oct 3, 2025
d991099
Merge branch 'dev' into renovate/astral-sh-ruff-pre-commit-0.x
mashehu Oct 3, 2025
973169f
Merge pull request #3791 from nf-core/renovate/astral-sh-ruff-pre-com…
mashehu Oct 3, 2025
836c4df
Merge branch 'dev' into renovate/textual-6.x
mashehu Oct 3, 2025
df37228
Merge branch 'dev' into 3747-fix-diff-printing
mashehu Oct 3, 2025
6198147
[automated] Update Textual snapshots
nf-core-bot Oct 3, 2025
4942d71
Merge pull request #3759 from awgymer/3747-fix-diff-printing
mashehu Oct 3, 2025
65d8e1a
Merge branch 'dev' into renovate/textual-6.x
mashehu Oct 3, 2025
b9302ca
update textual snapshots
mirpedrol Oct 3, 2025
89c6974
[automated] Update Textual snapshots
nf-core-bot Oct 3, 2025
95f62c2
Merge branch 'dev' into issues/3735-check-docker
mashehu Oct 3, 2025
dd7d929
Use the org from .nf-core.yml when linting multiqc_config report_comment
SZhengP Oct 4, 2025
d855b3e
[automated] Update CHANGELOG.md
nf-core-bot Oct 4, 2025
f0e8b8d
Merge pull request #3800 from nf-core/fix/lint_multiqc_org
SZhengP Oct 6, 2025
ad02984
update textual snapshot
mirpedrol Oct 6, 2025
cfb6fd4
override example keywords in modules test
mirpedrol Oct 6, 2025
c59c06e
[automated] Update CHANGELOG.md
nf-core-bot Oct 6, 2025
37418ee
Merge pull request #3801 from mirpedrol/lint-modules-example
mirpedrol Oct 6, 2025
d12381a
Merge branch 'dev' into update/mqc1.31
mirpedrol Oct 7, 2025
850944f
Merge pull request #3766 from nf-core/update/mqc1.31
mashehu Oct 7, 2025
a75e0c9
Merge branch 'dev' into renovate/textual-6.x
mashehu Oct 7, 2025
a22d22d
update textual snapshots
mirpedrol Oct 7, 2025
8f5de3b
Merge pull request #3793 from nf-core/renovate/textual-6.x
mashehu Oct 7, 2025
1c10f43
Merge branch 'dev' into issues/3735-check-docker
mashehu Oct 7, 2025
c5af93a
Update GitHub Actions (#3810)
renovate[bot] Oct 7, 2025
573e879
Update nf_core/pipelines/download/utils.py
JulianFlesch Oct 7, 2025
15d74bc
Update the utils_nfschema_plugin subworkflow to the latest version
nvnieuwk Oct 7, 2025
b0ba502
[automated] Update CHANGELOG.md
nf-core-bot Oct 7, 2025
86e185e
add link to lint test docs for modules and subworkflows
mirpedrol Oct 7, 2025
8f82914
Merge branch 'dev' into issues/3735-check-docker
JulianFlesch Oct 7, 2025
fc02ab8
Change to raising a DownloadError
JulianFlesch Oct 7, 2025
7bb65a8
Remove redundant error logging
JulianFlesch Oct 7, 2025
1ce4108
Merge branch 'dev' into issues/3729-download-cleanup
mashehu Oct 7, 2025
26f9884
update modules test assertions
mashehu Oct 7, 2025
12a4d47
[automated] Update CHANGELOG.md
nf-core-bot Oct 7, 2025
5fe18d9
update also subworkflow test template
mashehu Oct 7, 2025
ea8781d
remove `single_end` from modules test template
mashehu Oct 7, 2025
e499e94
Merge branch 'add-example-capture-to-modules-test' of github.com:mash…
mashehu Oct 7, 2025
a7749bb
[automated] Update CHANGELOG.md
nf-core-bot Oct 7, 2025
6886d36
Remove explicit tempdir cleanup
JulianFlesch Oct 7, 2025
e397d50
add finally to simplify
JulianFlesch Oct 7, 2025
c880f53
bump minimum python version to 3.10
mashehu Oct 8, 2025
18ba287
make ruff pass
mashehu Oct 8, 2025
243da69
add parent_lint_name for link generation
mirpedrol Oct 8, 2025
f86081e
[automated] Update CHANGELOG.md
nf-core-bot Oct 8, 2025
435164d
apply code suggestions
mashehu Oct 8, 2025
7a02ae6
Merge pull request #3750 from JulianFlesch/issues/3729-download-cleanup
JulianFlesch Oct 8, 2025
3e78524
Merge branch 'dev' into issues/3735-check-docker
JulianFlesch Oct 8, 2025
5f88de1
clean up imports
mirpedrol Oct 9, 2025
a5cd797
update test_environment_yml_sorting test
mirpedrol Oct 9, 2025
7fec804
Merge branch 'dev' into prettierignore-nftest
jonasscheid Oct 9, 2025
91d2c3e
[automated] Fix code linting
nf-core-bot Oct 9, 2025
998cf48
apply review comments by @mashehu
mirpedrol Oct 9, 2025
ffdfb5e
Merge pull request #3625 from jonasscheid/prettierignore-nftest
jonasscheid Oct 9, 2025
3307bfa
fix imports
mashehu Oct 9, 2025
4323c17
fix docstrings
mashehu Oct 9, 2025
664696c
Merge pull request #3814 from nvnieuwk/update/nf-schema-subwf
mashehu Oct 9, 2025
c91700f
Update dependency python to 3.14 (#3817)
renovate[bot] Oct 9, 2025
1da4e9c
update Dockerfile to python 3.14
mirpedrol Oct 9, 2025
db9c707
[automated] Update CHANGELOG.md
nf-core-bot Oct 9, 2025
a3a2bfb
Merge branch 'dev' into modules-lint-links
mirpedrol Oct 9, 2025
ccbcdd8
Merge pull request #3822 from mirpedrol/update-docker-file
mashehu Oct 9, 2025
e15bf4e
Merge pull request #3818 from mirpedrol/modules-lint-links
mirpedrol Oct 9, 2025
97371c3
Merge pull request #3752 from JulianFlesch/issues/3735-check-docker
JulianFlesch Oct 9, 2025
3afb111
Merge pull request #3815 from mashehu/add-example-capture-to-modules-…
mashehu Oct 10, 2025
faadb21
use same logic for super-tool selection in modules lint and bump-vers…
mashehu Oct 10, 2025
a054865
Merge branch 'dev' into update-to-python-3_10
mashehu Oct 13, 2025
095c8b5
Merge pull request #3816 from mashehu/update-to-python-3_10
mashehu Oct 13, 2025
4dacc4a
feat: Add codespaces badge to template README
JulianFlesch Oct 14, 2025
9052768
[automated] Update CHANGELOG.md
nf-core-bot Oct 14, 2025
d952b64
update pipeline template subworkflows
mirpedrol Oct 14, 2025
91bc6df
[automated] Update CHANGELOG.md
nf-core-bot Oct 14, 2025
65767e6
update changelog
mirpedrol Oct 14, 2025
3f09a86
template: fix launch action
mashehu Oct 14, 2025
6afd4a9
[automated] Update CHANGELOG.md
nf-core-bot Oct 14, 2025
e2413b8
Update CHANGELOG.md
mashehu Oct 14, 2025
15f5bfb
Merge pull request #3827 from mashehu/fix-launch-action
mashehu Oct 14, 2025
1ce7a5a
mock correct command in cache test
mashehu Oct 14, 2025
09f3ac4
Merge branch 'dev' into update-template-modules
mirpedrol Oct 14, 2025
a5411fa
Merge pull request #3826 from mirpedrol/update-template-modules
mirpedrol Oct 14, 2025
dfe5fcf
pipelines bump-version: fix indentation for list in dumped .nf-core.yml
mashehu Oct 14, 2025
d2faf1c
add test
mashehu Oct 14, 2025
5fc6e77
fix path
mashehu Oct 14, 2025
e73032f
[automated] Update CHANGELOG.md
nf-core-bot Oct 14, 2025
10bd3bc
remove ternary operators from container lines
mashehu Oct 15, 2025
245bbdc
[automated] Update CHANGELOG.md
nf-core-bot Oct 15, 2025
813dbf2
Merge pull request #3830 from mashehu/fix-ternary-containter-linting
mirpedrol Oct 15, 2025
4abeb06
Revert "Add .nf-test folder to prettierignore list"
mirpedrol Oct 15, 2025
ad09541
[automated] Update CHANGELOG.md
nf-core-bot Oct 15, 2025
1793280
Update CHANGELOG.md
mirpedrol Oct 15, 2025
1034e3c
Merge pull request #3831 from nf-core/revert-3625-prettierignore-nftest
mirpedrol Oct 15, 2025
e05da51
Merge pull request #3829 from mashehu/fix-list-indendation-of-bumped-yml
mashehu Oct 15, 2025
f0ae68b
bump to 3.4.0 for release
mirpedrol Oct 15, 2025
b15b298
Merge pull request #3832 from mirpedrol/bump-3.4.0
mirpedrol Oct 15, 2025
63a56af
Update CHANGELOG.md
mirpedrol Oct 15, 2025
425fdef
downgrade docker version to 3.13 in devcontainer
mashehu Oct 15, 2025
6622cf7
[automated] Update CHANGELOG.md
nf-core-bot Oct 15, 2025
dcf8835
Merge branch 'dev' into downgrade-py-version-in-devcontainer
mashehu Oct 15, 2025
ed58ed8
Update .devcontainer/build-devcontainer/Dockerfile
mashehu Oct 15, 2025
1ebee76
Merge pull request #3834 from mashehu/downgrade-py-version-in-devcont…
mashehu Oct 15, 2025
5703505
Fix: Add updated devcontainer config for template
JulianFlesch Oct 15, 2025
6a34d0d
Add changelog entry
JulianFlesch Oct 15, 2025
8fbe062
Change setup.sh script to be executable
JulianFlesch Oct 15, 2025
3d78b4b
Bump version
JulianFlesch Oct 15, 2025
bb19c8b
Add Path version to semantic version name
JulianFlesch Oct 15, 2025
4ff5df7
Update CHANGELOG.md
JulianFlesch Oct 15, 2025
7d06a73
Merge pull request #3835 from JulianFlesch/fix/template-devcontainer
mashehu Oct 15, 2025
f27651c
fix jinja template formatting for nextflow.config when skipping nf_co…
mirpedrol Oct 15, 2025
656637e
update changelog
mirpedrol Oct 15, 2025
fc5a933
Merge pull request #3836 from mirpedrol/jinja-nextflow-config
mirpedrol Oct 15, 2025
54e37e4
Merge branch 'dev' into issues/3751-codespaces-badge
mirpedrol Oct 16, 2025
5092409
Update nf_core/pipeline-template/README.md
JulianFlesch Oct 16, 2025
08524eb
Merge pull request #3824 from JulianFlesch/issues/3751-codespaces-badge
mirpedrol Oct 16, 2025
086cad4
Update CHANGELOG.md
mashehu Oct 16, 2025
0ddc346
Update CHANGELOG.md
mashehu Oct 16, 2025
6fb78b8
bump version to 3.5.0dev
mashehu Oct 16, 2025
6d6c996
Merge pull request #3839 from mashehu/bump-version-back
mashehu Oct 16, 2025
2852207
Merge branch 'dev' into capture-versions
mashehu Oct 24, 2025
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nf-core-bot committed Oct 1, 2025
commit 2ece3d6b73c69d2ee53c1ecc7b30028ed2f08710
1 change: 1 addition & 0 deletions CHANGELOG.md
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- Fix downloads: temporary files not moved and cleaned up correctly after singularity pull ([#3749](https://github.com/nf-core/tools/pull/3749))
- impr devcontainer: Add hostRequirements to run with 4CPUs and 16GB ram by default ([#3746](https://github.com/nf-core/tools/pull/3746))
- Add .nf-test/ to prettier ignore list ([#3776](https://github.com/nf-core/tools/pull/3776))
- Update dependency prompt_toolkit to <=3.0.52 ([#3783](https://github.com/nf-core/tools/pull/3783))

## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08]

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