1. 23 Apr, 2020 3 commits
  2. 22 Apr, 2020 11 commits
  3. 21 Apr, 2020 11 commits
  4. 20 Apr, 2020 5 commits
  5. 18 Apr, 2020 2 commits
    • van den Berg's avatar
      Add summary output for cutadapt · b8934d0a
      van den Berg authored
      The cutadapt summary file contains statistics we want to report, such as
      the number of reads and bases before and after trimming. This way, we do
      not need to compute these statistics after the fact, which would require
      parsing the large fastq files an additional time.
      b8934d0a
    • van den Berg's avatar
      No longer merge fastq files · 8670b32a
      van den Berg authored
      Instead of merging fastq files as the first step of the pipeline, merge
      as late as possible to make better use of parallelism, and to prevent
      unnecessary reading/writing of all data. Currently, reads are trimmed
      and mapped per read group, and are merge in the picard MarkDuplicates
      step. Therefore, samples are merged as a side effect of another task
      that was performed as well.
      
      Additionally, fastq processing is now done in a single step using
      cutadapt, instead of using both sickle and cutadapt sequentially.
      
      As part of these changes, the following changes were made:
       - Use cutadapt to trim both adapters and low quality reads
       - Run bwa align on each readgroup independently
       - Run fastqc on each readgroup independenly
       - Pass multiple bam files to picard MarkDuplicates
       - Remove safe_fastqc.sh script
       - Remove fastqc_stats
       - Remove fastqc coverage from covstats
       - Update test data for slight differences in output vcf files
       - Add tests for fastqc zip files
      8670b32a
  6. 17 Apr, 2020 2 commits
  7. 16 Apr, 2020 6 commits