Allow BAM/CRAM input #644
Description
Description of feature
Allowing BAM/CRAM input would make the pipeline more easily pluggable with other preprocessing pipelines.
Inputs that have BAM/CRAM files should skip the star alignment and only run tools that require BAM/CRAM files unless the FASTQ files are also given. A warning could help here to notify the user why some tools do not run (even though they were requested) with BAM/CRAM data. IMO adding a conversion subworkflow for BAM -> FASTQ is not really needed here as this should be done before running the pipeline if people want to run tools with FASTQ input