GitLab

* 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

* 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