fischuu/Pipeline-Holoruminant-Meta: 0.4.41

Breaking update! User needs to add to config/params.yaml under 'assemble' -> 'samtools' the entry out_type: "cram", otherwise there will be an error about a missing key. Please check the params.yaml in the default configuration of the pipeline. The background is that we had to introduce the option to use bam alignments (instead of cram), as for some datasets the cram header was too small resulting in pipeline crashes. If this happens, one can change here to the option out_type: "bam", which should solve the problem.