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Merged
mirpedrol merged 368 commits into from
Apr 28, 2023
Merged

Dev -> Master for v2.8 #2257

mirpedrol merged 368 commits into from
Apr 28, 2023

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@mirpedrol mirpedrol commented Apr 27, 2023

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

jfy133 and others added 30 commits March 23, 2023 10:21
@jfy133
Update usage.md
5fe0cb3
@jfy133 @mashehu
Apply suggestions from code review
638cc67 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@jfy133
Apply suggestions from code review
411327e
@jfy133
Apply suggestions from code review
4bc3f60
@jfy133
Merge pull request #2201 from nf-core/strip-resource-updates-template
7757347 
Pipeline template: condense main readme
@ewels
Fixed minor Jinja2 templating bug that caused the PR template to miss…
addcace 
… a newline
@ewels
Merge pull request #2209 from ewels/pr-template-fix
e3b3ed3 
Fixed minor Jinja2 templating bug
@awgymer
Add test for pipeline init with template yml
d88756b
@awgymer
Merge branch 'dev' into template-yml-to-file-on-create
87020c5
@awgymer
Add test mocking cli input
637e967
@awgymer
Add check to ensure output yml matches expected
326e600
@awgymer
Merge pull request #2189 from awgymer/template-yml-to-file-on-create
c655a60 
Dump template yml to file in pipeline repo after creation
@awgymer
Initial commit of system exit lint check
a8384a0
@fabianegli
deprecate Python 3.7 support
f6a19eb
@fabianegli
add link to PR
f3b5d1e
@awgymer
Add a small docstring. Add line number to lint message
1422b34
@awgymer
Add docs .md stub
8d70a77
@awgymer
Merge branch 'dev' into lint-system-exit
379e604
@awgymer
Allow System.exit(0) and update template
9626ae5
@anoronh4
Add failed lint condition when params.enable_conda is in a module
671c1e5
@anoronh4
Empty-Commit
d78b926
@anoronh4
fix code formatting with black
97fda70
@anoronh4
add tests to account for params.enable_conda failures
30a6dc3
@anoronh4
Add enable_conda linting to CHANGELOG
9559495
@anoronh4
Fix number of fails in assertion test
c2ab6fe
API spec of the different JSON schema fields
d19f64b
@aelezi01
Merge branch 'dev' into api_schema_description
fe63c0b
@awgymer
Initial commit of one method for patch removal
4659502
@aelezi01
Update README.md
a6623b1
@ewels
Updated AWS tests to use newly moved seqeralabs/action-tower-launch…
a3fa9d5 
… instead of `nf-core/tower-action`
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codecov bot commented Apr 27, 2023 •
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Codecov Report

Merging #2257 (7a7a326) into master (9e6b67f) will increase coverage by 1.67%.
The diff coverage is 81.37%.

@@            Coverage Diff             @@
##           master    #2257      +/-   ##
==========================================
+ Coverage   71.42%   73.10%   +1.67%     
==========================================
  Files          77       77              
  Lines        8367     8432      +65     
==========================================
+ Hits         5976     6164     +188     
+ Misses       2391     2268     -123
Impacted Files Coverage Δ
nf_core/bump_version.py 91.22% <ø> (+1.75%) ⬆️
nf_core/components/components_test.py 56.09% <0.00%> (-2.14%) ⬇️
nf_core/components/remove.py 84.81% <ø> (ø)
nf_core/download.py 52.72% <ø> (ø)
nf_core/launch.py 63.26% <ø> (ø)
nf_core/lint/files_unchanged.py 72.61% <ø> (ø)
nf_core/lint/nextflow_config.py 77.45% <ø> (ø)
nf_core/lint/template_strings.py 87.50% <ø> (ø)
nf_core/list.py 79.82% <ø> (ø)
nf_core/modules/__init__.py 100.00% <ø> (ø)
... and 24 more

... and 1 file with indirect coverage changes

@mirpedrol
Merge pull request #2258 from mirpedrol/change-gitpod-container
57a20b8 
Change gitpod container for 2.8 release
@mirpedrol mirpedrol marked this pull request as draft April 27, 2023 15:11
mirpedrol and others added 17 commits April 27, 2023 17:19
@mirpedrol
fix linting.yml from pipelines using python 3.8 instad of 3.7
7df7a0f
@mashehu
use the dev version of tools for the rich-codex images
fef0822
@mashehu
Merge pull request #2261 from mashehu/run-rich-with-dev
28555f2 
use the dev version of tools for the rich-codex images
@mirpedrol
Merge pull request #2260 from mirpedrol/linting-errors
501af49 
nf-core linting in pipeline uses python 3.8 instead of 3.7
@github-actions
Generate new screengrabs with rich-codex
5d8a3a7
@mirpedrol
Merge branch 'master' into dev
9f9e588
@mashehu
update modules in template
1879ff5
@mirpedrol
allow labels between single quotes
95d7ef3
@mirpedrol
Merge pull request #2263 from mashehu/fix-template-modules
fe2c5e8 
Update template modules
@mirpedrol
update dumpsoftwareversions permisions
c40ad45
@mirpedrol
Merge pull request #2264 from mirpedrol/update-dumpsoftwareversions
81e8278 
update dumpsoftwareversions permisions
@github-actions
Generate new screengrabs with rich-codex
df27c28
@mashehu
update subworkflow commands for rich-codex
b4f103c
@mashehu
Merge pull request #2265 from mashehu/fix-rich-code
20d0782 
Fix rich-codex previews for subworkflows
@github-actions
Generate new screengrabs with rich-codex
e48bb35
@mirpedrol
fix template new lines
7c6c51d
@mirpedrol
Merge pull request #2266 from mirpedrol/newline-fix
7a7a326 
fix template new lines
@mirpedrol mirpedrol marked this pull request as ready for review April 28, 2023 14:03
@mirpedrol mirpedrol merged commit 0912990 into master Apr 28, 2023
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