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* 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> |
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