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Antonie Vietor authored
* trimming with cutadapt added * additions to cutadapt according to View #1, BWA added as draft * adding cutadapt comments back, bwa mem will be moved to a new branch * mapping, duplicate marking and merging * changes according View #2 added, some minor additional changes with handling cutadapt-log-files for multiqc input in common.smk were necessary * code formatting with black * changes according view #2 added and replaced directory name mapped with merged in bwa_mem output, because its bam files are only temporary and otherwise the empty mapped directory would remain after the workflow-run * view #2: output path for rule bwa_mem and input path for rule merge_bams changed