* Make targets.bed optional when running in wgs mode
* added test for cram
* Update test_data_config with new reference.cnn
* Update main.nf to allow tumor-only running
Still need a unit-test for this. Almost ready, but needs this file as input https://github.com/nf-core/test-datasets/blob/modules/data/generic/cnn/reference.cnn
* re-writing previous changes, but now it wont crash the entire CI-setup
* fixing overlooked merge conflict
* last overlooked merge-conflict
* move all files to batch subfolder
* adding an optional input for a reference file (needed when running germline and tumoronly)
* minor typo
* update meta.yml
* aligning code, renaming cnvkit to cnvkit_batch, renaming tumorbam to tumor, normalbam to normal
* Update pytest_modules.yml
Co-authored-by: EC2 Default User <ec2-user@ip-172-31-21-198.us-west-2.compute.internal>
Co-authored-by: Lasse Folkersen <lassefolkersen@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
