• Antonie Vietor's avatar
    Mapping and duplicate marking (#2) · bb5a88a1
    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