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  • Antonie Vietor's avatar
    Filtering (#3) · 4607b5fc
    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
    * 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: