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

Real-data pytests #1017

Merged
merged 29 commits into from
Jul 5, 2024
Merged

Real-data pytests #1017

merged 29 commits into from
Jul 5, 2024

Conversation

WardDeb
Copy link
Member

@WardDeb WardDeb commented Jul 4, 2024

This PR initiates 'real data' tests. In brief:

  • Bumped all checkouts to V4
  • split up pytests from linux.yml
  • action runs mRNA-seq wf on subsetted fq file (included in the repo).

katsikora and others added 29 commits April 10, 2024 13:56
@katsikora
Merge pull request #1005 from maxplanck-ie/develop
0313d31 
Develop
Merge branch 'develop' of https://github.com/maxplanck-ie/snakepipes …
c480220 
…into develop
YAML, STARindex, config generated for mRNA-seq
8c7637c
test_mrna() modified
a586205
RNA-init
287e5af
@WardDeb
purge fa & gtf
6ec59be
@WardDeb
ignore fa and gtf files
82bbc05
@WardDeb
give pytests a separate action
618f03d
@WardDeb
include compressed fna & gtf
d1ec0e3
@WardDeb
init true mRNA run test
8127ab5
@WardDeb
rename pytest test
d51eb3f
@WardDeb
drop matrix from pytest
01051ef
@WardDeb
checkout v4
39f4343
@WardDeb
omit cluster config from data factory
1686875
@WardDeb
strings killing me slowly
cfdf2f2
@WardDeb
forgot comma
93462eb
@WardDeb
abspath for STARix
fd6b6cc
@WardDeb
starix and pytest in same job
7842ae5
@WardDeb
properly process startpath
49df787
@WardDeb
include a glob for outdir
caf1366
@WardDeb
add function for assert
ae80267
@WardDeb
omit micromamba cleanup from first shell
3b0227a
@WardDeb
move over checkouts to v4
a152325
@WardDeb
Merge branch 'develop' of github.com:maxplanck-ie/snakepipes into sna…
4ff4ed0 
…kepipes_pytest
test_mrna funct
3a0d2eb
test_mrna by Ward
31e8ec6
test with 4 samples
112c853
change paths rna test
fe83224
include mIFNB data dir
06399da
@WardDeb WardDeb requested a review from katsikora July 4, 2024 14:40
katsikora
katsikora reviewed Jul 5, 2024
View reviewed changes
Copy link
Contributor

@katsikora katsikora left a comment

Choose a reason for hiding this comment

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

Hey Ward,

am I reading this right that all of the build tests would be replaced by testing the mRNA-seq workflow only?

Best,
Katarzyna

@WardDeb
Copy link
Member Author

WardDeb commented Jul 5, 2024

Hey Ward,

am I reading this right that all of the build tests would be replaced by testing the mRNA-seq workflow only?

Best, Katarzyna

No, the build tests remain as they were before.
The pytests are moved into a separate action and now consist of:

  • jobcount dryruns (as they were before).
  • true run with real data (implemented in this PR).

katsikora
katsikora approved these changes Jul 5, 2024
View reviewed changes
Copy link
Contributor

@katsikora katsikora left a comment

Choose a reason for hiding this comment

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

Perfect, thanks!

@WardDeb WardDeb merged commit cb28234 into develop Jul 5, 2024
90 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@katsikora katsikora katsikora approved these changes

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
2 participants
@WardDeb @katsikora