1. 15 Jun, 2020 1 commit
    • 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: https://github.com/ewels/MultiQC/issues/512.
      4607b5fc
  2. 18 May, 2020 1 commit
    • 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
      bb5a88a1
  3. 30 Apr, 2020 1 commit
  4. 29 Apr, 2020 1 commit
  5. 28 Apr, 2020 1 commit
  6. 22 Apr, 2020 1 commit