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

TOPAS/GenConS #3662

Merged
merged 16 commits into from
Sep 29, 2023
Merged

TOPAS/GenConS #3662

merged 16 commits into from
Sep 29, 2023

Conversation

aidaanva
Copy link
Contributor

@aidaanva aidaanva commented Jul 21, 2023 •
edited
Loading

PR checklist

Closes #3641
Added new module for TOPAS/GenConS (https://github.com/subwaystation/TOPAS)

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

@aidaanva aidaanva requested a review from jfy133 July 21, 2023 09:44
jfy133
jfy133 requested changes Jul 21, 2023
View reviewed changes
Copy link
Member

@jfy133 jfy133 left a comment

Choose a reason for hiding this comment

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

Mostly there!

Just missing a couple of optional input/outputs and minor formatting :)

modules/nf-core/topas/gencons/main.nf Outdated Show resolved Hide resolved
modules/nf-core/topas/gencons/main.nf Outdated Show resolved Hide resolved
modules/nf-core/topas/gencons/meta.yml Outdated Show resolved Hide resolved
modules/nf-core/topas/gencons/meta.yml Show resolved Hide resolved
modules/nf-core/topas/gencons/meta.yml Outdated Show resolved Hide resolved
modules/nf-core/topas/gencons/main.nf Outdated Show resolved Hide resolved
tests/modules/nf-core/topas/gencons/main.nf Outdated Show resolved Hide resolved
tests/modules/nf-core/topas/gencons/main.nf Outdated Show resolved Hide resolved
modules/nf-core/topas/gencons/main.nf Outdated Show resolved Hide resolved
modules/nf-core/topas/gencons/main.nf Show resolved Hide resolved
@aidaanva aidaanva requested a review from jfy133 July 28, 2023 09:44
@jfy133 jfy133 added this pull request to the merge queue Jul 28, 2023
@jfy133 jfy133 removed this pull request from the merge queue due to a manual request Jul 28, 2023
@jfy133
Copy link
Member

jfy133 commented Jul 28, 2023

@aidaanva test fail is here

image

Firslty wierd that there is no prefix set (should be from a meta.id) but also as the md5sum gets violated via conda (normally solved by -n), we may need to replace the md5sum with a string the header of the VCF file (pyest can read GZ files so should be OK)

@subwaystation
Copy link
Contributor

What a surprise that this is still used!! :)

@SPPearce
Copy link
Contributor

@aidaanva , do you need help to finish this module off?

@jfy133
Copy link
Member

jfy133 commented Sep 25, 2023

Aida is my partner (therefore also currently on parental leave 😬) so that would be extremely helpful if you had time @SPPearce !

@SPPearce
Copy link
Contributor

Aah, didn't know that, hope you are both enjoying the time with your child! I'll take a look at the outstanding issue.

@SPPearce
Copy link
Contributor

Ok, I think it is ready. The input meta's were all called meta, which is why the prefix wasn't being set properly. I've also set the vcf as a contains to stop conda whinging.

jfy133
jfy133 approved these changes Sep 29, 2023
View reviewed changes
modules/nf-core/topas/gencons/main.nf
def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

"""

Copy link
Member

Choose a reason for hiding this comment

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

Suggested change

@SPPearce SPPearce added this pull request to the merge queue Sep 29, 2023
Merged via the queue into nf-core:master with commit 29595ea Sep 29, 2023
10 checks passed
@jfy133
Copy link
Member

jfy133 commented Sep 29, 2023

Thank you very much @SPPearce !!

snesic pushed a commit to JPejovicApis/modules that referenced this pull request Oct 10, 2023
@aidaanva @jfy133
@adamrtalbot @SPPearce @snesic
TOPAS/GenConS (nf-core#3662)
ba8939b 
* added topas/gencons tests

* finish tests

* run prettier

* modify test new input gatk ug

* Update modules/nf-core/topas/gencons/main.nf

Co-authored-by: James A. Fellows Yates <[email protected]>

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <[email protected]>

* updated input, output and test after review

* Fix meta and Update tests

* Prettify

---------

Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: Adam Talbot <[email protected]>
Co-authored-by: Simon Pearce <[email protected]>
lrauschning pushed a commit to lrauschning/modules that referenced this pull request Oct 16, 2023
@aidaanva @jfy133
@adamrtalbot @SPPearce
TOPAS/GenConS (nf-core#3662)
6471b4a 
* added topas/gencons tests

* finish tests

* run prettier

* modify test new input gatk ug

* Update modules/nf-core/topas/gencons/main.nf

Co-authored-by: James A. Fellows Yates <[email protected]>

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <[email protected]>

* updated input, output and test after review

* Fix meta and Update tests

* Prettify

---------

Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: Adam Talbot <[email protected]>
Co-authored-by: Simon Pearce <[email protected]>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jfy133 jfy133 jfy133 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.

new module: TOPAS/GenConS
5 participants
@aidaanva @jfy133 @subwaystation @SPPearce @adamrtalbot