1. 07 May, 2021 2 commits
  2. 03 May, 2021 1 commit
  3. 27 Apr, 2021 3 commits
  4. 09 Mar, 2021 4 commits
  5. 27 Nov, 2020 1 commit
    • van den Berg's avatar
      Update jinja template to use floats instead of int · c620561d
      van den Berg authored
      This fixes a crash in the generation of the pdf report when there is
      expression of the MECOM gene. If there is MECOM expression, the read
      counts are actually floats, not integers, which leads to a crash.
      c620561d
  6. 29 Oct, 2020 1 commit
  7. 04 Aug, 2020 2 commits
    • van den Berg's avatar
      Close quote in Readme · f69efaa1
      van den Berg authored
      f69efaa1
    • van den Berg's avatar
      Extend the Readme · 4cab884b
      van den Berg authored
      Add explanation on how to run the pipeline and the importance of using
      the --use-singularity flag.
      
      Add an example on manually running one of the test cases.
      
      Add an explanation on the different branches and how to use them.
      4cab884b
  8. 29 Jul, 2020 3 commits
  9. 27 Jul, 2020 1 commit
    • van den Berg's avatar
      Add github link to readme, and remove graph · a172279a
      van den Berg authored
      Since external users cannot submit issues or pull requests without an
      account for the LUMC gitlab instance, we should refer them to the public
      github instance of HAMLET.
      
      The pipeline graph doesn't add a lot of information, and it doesn't
      render on github, so it was removed.
      a172279a
  10. 01 Jul, 2020 1 commit
  11. 25 Jun, 2020 2 commits
  12. 24 Jun, 2020 2 commits
  13. 23 Jun, 2020 2 commits
  14. 17 Jun, 2020 1 commit
  15. 12 Jun, 2020 3 commits
  16. 03 Jun, 2020 3 commits
    • van den Berg's avatar
      Add test for RUNX1 insertion · b77977e1
      van den Berg authored
      This tests the fix for #issue-11, which was resolved by a new upstream release
      of the gmap aligner. The same upstream release also fixes #issue-12.
      b77977e1
    • van den Berg's avatar
      Add tests data for duplication in RUNX1 · 3610caf9
      van den Berg authored
      3610caf9
    • van den Berg's avatar
      Upgrade gsnap to version 20.06.01 · 734b19b1
      van den Berg authored
       - Upgrade pytest-workflow to version 1.4.0, which adds support for
         contains_regex.
       - Update test cases to match the values produced by the new version of gsnap.
         Use contains_regex to reduce the sensitivity of the test cases to small
         changes in values.
       - Change the MV4-11 FLT3 hotspot mutation test to a different variant. The
         previous variant was in a hard to map region, so it is unclear if it is an
         error when it could not be found.
      734b19b1
  17. 18 May, 2020 1 commit
  18. 14 May, 2020 1 commit
  19. 13 May, 2020 2 commits
  20. 12 May, 2020 1 commit
  21. 06 May, 2020 1 commit
  22. 29 Apr, 2020 2 commits