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Merged
mirpedrol merged 51 commits into from
Dec 19, 2022
Merged

Dev -> Master for v2.7.2 #2136

mirpedrol merged 51 commits into from
Dec 19, 2022

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@mirpedrol mirpedrol commented Dec 19, 2022

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

mirpedrol and others added 30 commits December 8, 2022 14:13
@mirpedrol
bump to v2.8dev
51587c0
@mirpedrol
Merge pull request #2113 from mirpedrol/2.8dev
f8eab49 
bump to v2.8dev
@mirpedrol
Merge branch 'master' of https://github.com/nf-core/tools into dev
60e7cc5
@mirpedrol
fix github_output syntax
46317bd
@mirpedrol
update changelog
78d4a25
@mirpedrol
Merge pull request #2114 from mirpedrol/github-output
67e3702 
fix github_output syntax on GHA
@awgymer
Return from get_username and make sure it is assigned back to self.au…
0d7925b 
…thor
@mirpedrol
allow specifying only one container
2cd002c
@mirpedrol
modify changelog
96826eb
@awgymer
Merge pull request #2120 from awgymer/fix-component-author
3dc4052 
Ensure component author is properly captured and stored
@awgymer
Ensure call to load_tools_config expects tuple return
a8cc7d9
@awgymer
Merge pull request #2122 from awgymer/fix-lint-pipeline-name
94a03a1 
Fix lint pipeline name
@mirpedrol
check only one container per line
a85b896
@mirpedrol
Merge branch 'dev' of https://github.com/nf-core/tools into dev
2b96d32
@mirpedrol
only check pipeline name without dashes if the name is provided by pr…
6a7da79 
…ompt
@mirpedrol
Merge pull request #2121 from mirpedrol/dev
bc44d2e 
allow specifying only one container
@mirpedrol
Merge branch 'dev' of https://github.com/nf-core/tools into dev
ffc3bd3
@mirpedrol
Merge branch 'dev' of https://github.com/mirpedrol/tools into dashed-…
d97e116 
…name
@mirpedrol
run prettier after dumping a json schema file
f05b06e
@mirpedrol
modify changelog
a0f5d56
@mirpedrol
update changelog
5ccbae8
@ewels
Merge pull request #2123 from mirpedrol/dashed-name
ed9cbb4 
only check pipeline name without dashes if the name is provided by prompt
@mashehu
add newline before table 🤞🏻
e9e039a
@mashehu @ewels
Update README.md
e3d987e 
Co-authored-by: Phil Ewels <[email protected]>
@nf-core-bot
[automated] Fix code linting
5338afb
@mashehu
Update README.md
6e7f87a
@mashehu
Merge pull request #2128 from mashehu/fix-table-in-readme
e178898 
add newline before table 🤞🏻
@mirpedrol @ewels
Apply suggestions from code review
47b4252 
Co-authored-by: Phil Ewels <[email protected]>
@mirpedrol
merge branch dev
8d083d4
@mirpedrol
add json.dump into a helper function
6eb4664
mirpedrol and others added 21 commits December 15, 2022 09:38
@mirpedrol
Merge pull request #2124 from mirpedrol/prettier-json-schema
10b2b7f 
run prettier after dumping a json schema file
@mirpedrol
remove params.enable_conda
433e5b2
@mirpedrol
add params.enable_conda to deprecated vars
547076b
@mirpedrol
update CHANGELOG
d9be489
@mirpedrol
update pipeline template modules
4cf1fdc
@mirpedrol
fix test
c83965d
@mirpedrol
fix test
3b2f53d
@ewels
Revert unique() syntax change. Closes #2132
8acc9d6
@ewels
Merge pull request #2133 from ewels/revert-unique-change
ee6725a
@mirpedrol
Merge branch 'dev' of https://github.com/nf-core/tools into handle-js…
ccdd515 
…on-exception
@mirpedrol
handle json exception
8ce4d17
@mirpedrol
handle all json-load exceptions
67c3656
@mirpedrol
update CHANGELOG
1625014
@mirpedrol
remove handling from linting as it's already handled later
632b675
@mirpedrol
Merge branch 'dev' of https://github.com/nf-core/tools into conda-enable
32bf4aa
@mirpedrol
check conda channels as it's done in rnaseq
0cb35e6
@mirpedrol
remove params.enable_conda from modules template
81fc966
@drpatelh
Merge pull request #2131 from mirpedrol/conda-enable
b33d0c7 
Remove params.enable_conda
@mirpedrol
Merge pull request #2134 from mirpedrol/handle-json-exception
d45b8e3 
Handle json.load() exceptions
@mirpedrol
bump to 2.7.2 for patch release
02acf65
@mirpedrol
Merge pull request #2135 from mirpedrol/bump-2.7.2
9e6b67f 
Bump to 2.7.2
@codecov
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codecov bot commented Dec 19, 2022 •
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Codecov Report

Merging #2136 (9e6b67f) into master (54aee22) will increase coverage by 3.44%.
The diff coverage is 74.35%.

@@            Coverage Diff             @@
##           master    #2136      +/-   ##
==========================================
+ Coverage   67.97%   71.42%   +3.44%     
==========================================
  Files          43       77      +34     
  Lines        5633     8367    +2734     
==========================================
+ Hits         3829     5976    +2147     
- Misses       1804     2391     +587
Impacted Files Coverage Δ
nf_core/lint/nextflow_config.py 77.45% <ø> (ø)
nf_core/sync.py 75.10% <0.00%> (-0.32%) ⬇️
nf_core/utils.py 82.38% <50.00%> (ø)
nf_core/modules/lint/main_nf.py 65.72% <57.14%> (-0.47%) ⬇️
nf_core/modules/modules_json.py 80.26% <66.66%> (ø)
nf_core/create.py 65.01% <75.00%> (ø)
nf_core/components/components_create.py 75.00% <100.00%> (+0.23%) ⬆️
nf_core/launch.py 63.26% <100.00%> (-0.10%) ⬇️
nf_core/lint_utils.py 80.76% <100.00%> (+2.04%) ⬆️
nf_core/modules/create.py 84.95% <100.00%> (ø)
... and 40 more

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mashehu
mashehu approved these changes Dec 19, 2022
View reviewed changes
@mirpedrol mirpedrol merged commit 9d7dbee into master Dec 19, 2022
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7 participants

@mirpedrol @mashehu @awgymer @ewels @nf-core-bot @drpatelh