* 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 * rule for samtools view added * rule samtools_view added, rules for samtools_index, flagstat, idxstats and samtools_stats were created as drafts and are therefore still commented out * adding filtering rules, rule for removing orphan reads, adding rule for samtools sorting and statistics for multiqc * Higher parallelization of the stats rules by outsourcing general rules for this purpose in stats.smk and utils.smk. Statistics for multiqc input of BAM files after 'bwa_mem' and 'merge_duplicates' added. * Changes according to View #3. * refactoring _dedup * Log-path refactoring according to view #3. In multiqc-report the hovering of data points for samtools stats, flagstat and idxstats works for Chromium browser, but not for Firefox. Additional plots can be generated from the multiqc_data statistics, as described here: https://github.com/ewels/MultiQC/issues/512.