1. 26 Aug, 2020 1 commit
  2. 25 Aug, 2020 6 commits
  3. 24 Aug, 2020 5 commits
  4. 21 Aug, 2020 19 commits
  5. 20 Aug, 2020 1 commit
  6. 12 Aug, 2020 2 commits
    • van den Berg's avatar
      Remove directory output from fastqc · 89da42b6
      van den Berg authored
      The directory output for the fastqc tasks is causing issues on the
      shared file system of the cluster, since it cannot properly determine
      the age of the folder. As a result, it re-runs the fastqc tasks every
      time a workflow is restarted, regardless of whether the task has already
      completed.
      
      To prevent this, a single dummy output file '.done' has been added to
      the fastqc tasks which will be written when fastqc exits successfully.
      89da42b6
    • van den Berg's avatar
      e76c3b7b
  7. 07 Aug, 2020 3 commits
    • van den Berg's avatar
      Add an option to restrict BaseRecalibration · e33b4498
      van den Berg authored
      The base recalibration (BQSR) step of the pipeline can take up to 7 hours for
      WGS samples, which is a significant part of the total run time.
      
      The developers of GATK state that BQSR requires at least 100M bases per read
      group: "We usually expect to see more than 100M bases per read group; as a rule
      of thumb, larger numbers will work better."
      
      A human WGS sample with an average read depth of 43x has almost 1300 times that
      amount of bases. The analysis of these samples would be sped up greatly by
      restricting BQSR to a single chromosome.
      e33b4498
    • van den Berg's avatar
      Add an option to restrict BaseRecalibration · 095305f0
      van den Berg authored
      The base recalibration step of the pipeline can take up to 7 hours for
      WGS samples, which is a significant part of the total run time.
      
      The developers of GATK state that BQSR requires at least 100M bases per
      read group: "We usually expect to see more than 100M bases per read
      group; as a rule of thumb, larger numbers will work better."
      
      A human WGS sample with an average read depth of 43x has almost 1300
      times that amount of bases. The analysis of these samples would be sped
      up greatly by restricting BQSR to a single chromosome.
      095305f0
    • van den Berg's avatar
      Speed up cutadapt · b585ff80
      van den Berg authored
      Use 8 cores instead of just 1, according to the documentation speed
      should almost scale linear with the cores provided.
      
      Also reduce the compression level on the output file, since most time
      for cutadapt is spent re-compressing the data after trimming the
      adapters.
      b585ff80
  8. 29 Jul, 2020 2 commits
  9. 28 Jul, 2020 1 commit