1. 17 Apr, 2020 1 commit
  2. 16 Apr, 2020 7 commits
  3. 15 Apr, 2020 1 commit
    • van den Berg's avatar
      Remove global python variables · 7da15fdb
      van den Berg authored
      To make the pipeline more robust, the global python variables for
      various settings were removed where possible. Their values have been
      moved to the configuration json file, and a jsonschema validation has
      been added to the pipeline to make sure the configuration is valid.
      
      The downsampling step using seqtk has been remove since it was not used.
      
      The following additional changes were made:
       - Remove all --config values except CONFIG_JSON
       - Extend the config schema with the required and optional files that
         are supported
       - Add jsonschema validation of CONFIG_JSON
       - Remove global variables for scripts, add them to settings
         dictionary
       - Remove global variable for SAMPLES, use the settings dictionary
         instead
       - Remove support for multiple bed files
       - Remove support for multiple refFlat files
       - Remove support for downsampling of reads
       - Add json and jsonschema to the requirements
       - Update tests to work with the new config file
      7da15fdb
  4. 08 Apr, 2020 1 commit
  5. 07 Apr, 2020 2 commits
  6. 06 Apr, 2020 2 commits
  7. 03 Apr, 2020 2 commits
  8. 01 Apr, 2020 1 commit
  9. 31 Mar, 2020 5 commits
  10. 30 Mar, 2020 3 commits
  11. 14 Jan, 2020 1 commit
    • van den Berg's avatar
      Use local tmp folder as java tempdir · 3c5edeb2
      van den Berg authored
      This fixes a rare bug where picard runs out of disk space on when spilling
      reads to disk, because it uses the internal java temp dir as a location. This
      closes issue #42
      3c5edeb2
  12. 13 Jan, 2020 1 commit
  13. 10 Jan, 2020 2 commits
  14. 09 Jan, 2020 3 commits
  15. 08 Jan, 2020 2 commits
  16. 20 Dec, 2019 2 commits
  17. 19 Dec, 2019 3 commits
    • van den Berg's avatar
      Add threads entry for additional fastq rule · 1c34bfc0
      van den Berg authored
      1c34bfc0
    • van den Berg's avatar
      Add threads to fastqc · 9f6eafed
      van den Berg authored
      Hutspot sometimes fails on the fastqc analysis due to Java heap space
      memory errors. It is not possible to set the memory usage by fastqc
      directly, since this is done by the perl wrapper script. However, the
      amount of memory that is set by the wrapper scales with the number of
      threads that fastqc uses. Therefore, the number of threads was
      increased, effectively increasing the memory fastqc can use.
      9f6eafed
    • van den Berg's avatar
      Increase vmem limit for multiqc · 17397839
      van den Berg authored
      17397839
  18. 12 Nov, 2019 1 commit