Dev -> Master for v2.4 release #1581
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Bump 2.4dev
Fix bug in readme logo path
Noticed that when there are more dots in the FASTQ file name, the Path(file).suffixes returns all elements split by dot, which ends in list mismatch, therefore throwing an error. I think we should limit it to the last two items (according to VALID_FORMATS) for the extension check. Hope this PR helps to solve the problem.
Fix: Get file extensions correctly in validate_pair
Add a last newline to modules.json to avoid prettier error
Tower.nf is now running Nextflow 22.03.0.edge by default, which includes a new strategy to handle retrying jobs killed due to AWS spot policies. This was the reason for these lines of config, so they can now be removed.
Remove nextflow_config from AWS test CI
Add last line to json files
Direct copy of .gitignore. Hopefully can get rid of this file again one day, see prettier/prettier#4708
Add .prettierignore file
Escaped test run output before logging it, to avoid a rich `MarkupError`
- Move the {% endraw %} statements off comment lines and on to the tail of the last statement to get rid of flating comment marker
- Remove quotes around the master branch check to try to fix action
GH Actions workflow YAML tweaks.
Also check that only script or shell used and not both.
Module lint styling
Module linting: Only lint script if there was a script.
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
- Remove black backgrounds. Now that GitHub has dark mode, they dissapear into the background. - Add a badge to launch on Tower
Module lint: Allow no input or output in YAML
Readme badges update
Prepare v2.4 release
Codecov Report
@@ Coverage Diff @@
## master #1581 +/- ##
==========================================
- Coverage 64.85% 64.64% -0.22%
==========================================
Files 52 54 +2
Lines 6055 6253 +198
==========================================
+ Hits 3927 4042 +115
- Misses 2128 2211 +83
Continue to review full report at Codecov.
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Don't think I know enough python to approve. I tried syncing the testpipeline though, and that worked really well: nf-core/testpipeline#40
(Only fail, because I adapted the linting.yml to use the dev version. then it doesn't match the template and the linting rightfully complains)
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Oh nice, thanks! I want to do a sync test where it automatically creates the PR for me still (it's that stuff with the GitHub API that I refactored) but a relief to know that the sync itself isn't playing up 😅 |
Update gitpod image
drpatelh
approved these changes
May 16, 2022
JoseEspinosa
approved these changes
May 16, 2022
Fix header sniffing
Release review fixes
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PR checklist
CHANGELOG.mdis updateddocsis updated