Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[skip ci] Dev -> Master for 3.15.0 #1258

Open
wants to merge 415 commits into
base: master
Choose a base branch
from
Open

[skip ci] Dev -> Master for 3.15.0 #1258

wants to merge 415 commits into from
+29,396 −5,792

Conversation

drpatelh
Copy link
Member

  • Adds nf-test to all components of pipeline

maxulysse and others added 30 commits March 4, 2024 19:26
@maxulysse
add meta map
8a0776a
@maxulysse
fix cardinality
11d1a05
@maxulysse
typo:tyop
b42c8f6
@maxulysse
Merge pull request #1221 from adamrtalbot/nf-test-cicd
a50212c 
Add all nf-core modules and CI/CD and all nf-tests to everything
@maxulysse
Merge branch 'dev' into sortmerna
5dd8adb
@maxulysse
update CHANGELOG
d02c6f6
@maxulysse
fix path
d0941f1
@maxulysse @pinin4fjords
Update subworkflows/local/prepare_genome/main.nf
04b3581 
Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>
@maxulysse
Merge pull request #1231 from maxulysse/sortmerna
34e51dd 
Update sortmerna usage
@maxulysse
copy tests from star_genomegenerate
341fb5d
@maxulysse
Merge branch 'dev' into star_igenomes
e67f55a
@maxulysse
more descriptive tests' names
4d9e2fb
@maxulysse
Merge pull request #1232 from maxulysse/star_igenomes
4ef4025 
Adding tests for star_align igenomes
@maxulysse
add nf-tests for star_align_igenomes
7fa04bb
@pinin4fjords
Switch to genomecov from nf-core (with separate sort)
968cf9c
@pinin4fjords
Fix config import
e9a5ba8
@maxulysse
push tests
66848be
@pinin4fjords
Add missing inputs, closures
c624bfe
@pinin4fjords
Remove trailing whitespace
5f9d3ce
@pinin4fjords
genomecov from modules
e667765
@pinin4fjords
pretter on modules.json
11b11b2
@pinin4fjords
Fix tests
6db4979
@pinin4fjords
Bump modules
5e412b1
@pinin4fjords
Fix final test data path- update modules.json later
7c89af8
@pinin4fjords
Update CHANGELOG
58fbfad
@pinin4fjords
Final genomecov test fix
cbb9d53
@pinin4fjords
Merge pull request #1234 from nf-core/bedtools_genomecov_from_nfcore
14c8698 
Switch to genomecov from nf-core
@adamrtalbot
Add nf-tests for nf-core/rnaseq utility functions
18fcdbd 
Changes:
 - Change function name from validateInputSamplesheet to checkSamplesAreConsistent to accurately reflect what the function is doing
 - Add nf-tests for all functions in UTILS_NFCORE_RNASEQ_PIPELINE
@adamrtalbot
Adds tests for nf-core/rnaseq utility subworkflows
c988ce0 
Changes:
 - Makes nextflow_schema.json a parameter so we can actually set it. Not exposed right now but will be.
 - Adds basic tests that check for correct running only. Defaults to lots of stuff off.

We should extend this to check for more things but we're in a rush right now.
@adamrtalbot
Merge branch 'dev' into nf-test-utils_nfcore_rnaseq_pipeline
fce6bfb
maxulysse and others added 18 commits April 10, 2024 19:03
@maxulysse
Merge pull request #1282 from adamrtalbot/fixup_changelog_error
9e4cf57 
Fix CHANGELOG error
@adamrtalbot
CHANGELOG
651c755
@adamrtalbot
Merge branch 'dev' into increase_coverage_of_default_test_snapshot
abb3afb
@adamrtalbot
Remove variable files from default pipeline snapshot
9d281ab
@adamrtalbot
update snap
4c0ac4c
@maxulysse
Merge branch 'dev' into getGenomeAttribute
71ef0f5
@adamrtalbot
Remove more from snaps
b903195
@maxulysse
feat(igenomes): update name as in template
d62e208
@maxulysse
feat(references): fix usage of igenomes references
a54300a
@maxulysse
no need for key
8f3603a
@adamrtalbot
Merge pull request #1283 from adamrtalbot/increase_coverage_of_defaul…
d129b5a 
…t_test_snapshot

Increase contents of default.main.nf.test.snap
@maxulysse
remove tests for functionned removed
17767e1
@MatthiasZepper
Improve the extra_args parameter consolidation so it can override pre…
fbaef17 
…sets from the config.
@MatthiasZepper
Changelog update.
0d7e0f5
@MatthiasZepper
Implement Jonathan Manning's map-method for extra argument consolidat…
934019e 
…ion for the local STAR alignment subworkflow.
@MatthiasZepper
Implement Jonathan Manning's map-method for extra argument consolidat…
8027585 
…ion for the FastQC-UMItools-Trimgalore subworkflow..
@MatthiasZepper @pinin4fjords
Apply @pinin4fjords (Jonathan Manning)'s suggestions from code review
6ab2e44 
Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io>
@MatthiasZepper
Merge pull request #1248 from MatthiasZepper/ExtraArgsConsolidation
dcd5659 
Improved ext.args consolidation for STAR and TRIMGALORE
adamrtalbot
adamrtalbot reviewed Apr 18, 2024
View reviewed changes
.github/python/find_changed_files.py
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

We can possibly replace this with https://github.com/adamrtalbot/detect-nf-test-changes/ but it's very early days!

maxulysse and others added 11 commits April 22, 2024 12:38
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@adamrtalbot adamrtalbot adamrtalbot left review comments

At least 2 approving reviews are required to merge this pull request.

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
7 participants
@drpatelh @adamrtalbot @maxulysse @pinin4fjords @robsyme @MatthiasZepper @nf-core-bot