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nf-core
Repository to host tool-specific module files for the Nextflow DSL2 community!
This will add a subworkflow to follow the gatk4 best practices for aligning and preprocessing sequencing data to be used for the gatk variant calling workflows (joint germline, tumour normal,...
## 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**...
This subworkflow will cover the gatk4 best practices workflow: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- starting with the analysis ready reads of multiple individual samples*, haplotypecaller is then run in gvcf mode for each sample,...
### Is there an existing module for this? - [X] I have searched for the existing module ### Is there an open PR for this? - [X] I have searched...
Related to https://github.com/nf-core/modules/issues/2154 Manually inspected the following using `TMPDIR=~ nf-core modules test` for Docker, Singularity and Conda. - [x] amrfinderplus/run - [x] amrfinderplus/update - [x] ariba/run - [x] busco -...
### Have you checked the docs? - [X] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [X] [nf-core modules documentation](https://nf-co.re/docs/contributing/modules) ### Description of the bug Hi, when doing tests I got this warning: ```...
Add a requirement for a (mermaid) diagram to subworkflow docs. This diagram should be added to a readme doc inside the subworkflow dir.
