modules
modules copied to clipboard
Add subworkflow: gatk joint germline calling
PR checklist
Closes #1126
Adds joint germline variant calling subworkflow. Based on Gatk best practices for joint germline calling. Do not merge until the checklist in 1126 is finished
- [x] This comment contains a description of changes (with reason).
- [x] If you've fixed a bug or added code that should be tested, add tests!
- [x] If you've added a new tool - have you followed the module conventions in the contribution docs
- [x] If necessary, include test data in your PR.
- [x] Remove all TODO statements.
- [x] Emit the
versions.yml
file. - [x] Follow the naming conventions.
- [x] Follow the parameters requirements.
- [x] Follow the input/output options guidelines.
- [x] Add a resource
label
- [x] 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:
- [x]
PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd
- [x]
PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd
- [x]
PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd
- [x]
Won't be able to merge it in until the cl tests are back up again. But here is where it is so far
wonderful wonderful! thanks everyone for the hard work on this!!
Oh on problem I see now, is that I updated a bunch of gatk modules over Christmas , that use intervals, because we usually have multiple intervals per patient. Sorry about that. So I believe the input for some of them need to be adapted, like Haplotypecaller for example will have the interval
within the input
(sorry about that @GCJMackenzie 😢 )
Hi there!
We've noticed there hasn't been much activity here. Are you still planning on working on this? If not, you can ignore this message and we'll close your PR in about 2 weeks
Cheers the nf-core maintainers