Commits · 42d202505b0627a8d62554f1d738f535ee7d6c16 · Klinische Genetica / capture-lumc / hutspot · GitLab

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Aug 25, 2020
- Shorten test names · 42d20250
  van den Berg authored Aug 25, 2020
  
  42d20250
- No longer hide script paths in config · ea8629eb
  van den Berg authored Aug 25, 2020
  
  ea8629eb
- Add localrules if rules take less then 5 seconds · ae68936e
  van den Berg authored Aug 25, 2020
  
  ae68936e
Aug 24, 2020
- Only run FastQC on the trimmed file · 8a6c6da6
  van den Berg authored Aug 24, 2020
  
  8a6c6da6
- Remove custom statistics in favor of picard · c6cadb60
  van den Berg authored Aug 24, 2020
  
  c6cadb60
- Use samtools to sort bamfile · d563632b
  van den Berg authored Aug 24, 2020
  
  d563632b
- Merge branch 'speedup' of https://git.lumc.nl/klinische-genetica/capture-lumc/hutspot into speedup · 9255d5f5
  van den Berg authored Aug 24, 2020
  
  9255d5f5
- Merge branch 'devel' into speedup · 084797bb
  van den Berg authored Aug 24, 2020
  
  084797bb
Aug 21, 2020
- Remove python imports from the main snakemake file · ecc12cc2
  van den Berg authored Aug 21, 2020
  
  ecc12cc2
- Make formatting more consistent · 5f215391
  van den Berg authored Aug 21, 2020
  5f215391
- Add snakemake linting · 36fb2f9b
  van den Berg authored Aug 21, 2020
  
  36fb2f9b
- Move final functions to separate file · e1e83b13
  van den Berg authored Aug 21, 2020
  
  e1e83b13
- Clean up input for multiqc · 9ab0debe
  van den Berg authored Aug 21, 2020
  
  9ab0debe
- Move cutadapt summary files to separate file · 88c13809
  van den Berg authored Aug 21, 2020
  
  88c13809
- Move gathering after scatter to separate file · 79de4b37
  van den Berg authored Aug 21, 2020
  
  79de4b37
- Add test for input multiple readgroups · 4f5695d8
  van den Berg authored Aug 21, 2020
  4f5695d8
- Move markdup inputs to separate file · 1ce11c64
  van den Berg authored Aug 21, 2020
  
  1ce11c64
- Clean up input for rule 'all' · f16a49c1
  van den Berg authored Aug 21, 2020
  
  f16a49c1
- Begin moving python code into separate file · 383b838f
  van den Berg authored Aug 21, 2020
  
  383b838f
- Add gatk_jar to schema · 2e1aac68
  van den Berg authored Aug 21, 2020
  
  2e1aac68
- Use python f-string for formatting · 0dff1b37
  van den Berg authored Aug 21, 2020
  
  0dff1b37
- Remove explicit path from params for linting · aa37905b
  van den Berg authored Aug 21, 2020
  
  aa37905b
- More hiding for the linter · f1f323f5
  van den Berg authored Aug 21, 2020
  
  f1f323f5
- Hide the absolute path for GATK for linting · b1780fe9
  van den Berg authored Aug 21, 2020
  
  b1780fe9
- Add separate logfiles for different commands · a948a75c
  van den Berg authored Aug 21, 2020
  
  a948a75c
- Add log to every rule, this allows for linting · 515c9743
  van den Berg authored Aug 21, 2020
  
  515c9743
- Update snakemake version · 50989904
  van den Berg authored Aug 21, 2020
  
  50989904
Aug 20, 2020
- Add resources to tasks · 665d6d1f
  van den Berg authored Aug 20, 2020
  
  665d6d1f
Aug 12, 2020
- Remove directory output from fastqc · 89da42b6
  van den Berg authored Aug 12, 2020
  89da42b6
- Install hutspot environment when it doesn't exist · e76c3b7b
  van den Berg authored Aug 12, 2020
  
  e76c3b7b
Aug 07, 2020
- Add an option to restrict BaseRecalibration · e33b4498
  van den Berg authored Aug 7, 2020
  e33b4498
- Add an option to restrict BaseRecalibration · 095305f0
  van den Berg authored Aug 7, 2020
  095305f0
- Speed up cutadapt · b585ff80
  van den Berg authored Aug 7, 2020
  b585ff80
Jul 29, 2020
- Increase runtime for tests to 30 minutes · 1d79ec4c
  van den Berg authored Jul 29, 2020
  
  1d79ec4c
- Mark FastQC input for MultiQC as directory · 3481d929
  van den Berg authored Jul 29, 2020
  
  3481d929
Jul 28, 2020
- Merge branch 'devel' of https://git.lumc.nl/klinische-genetica/capture-lumc/hutspot into devel · 81e3bcf2
  van den Berg authored Jul 28, 2020
  
  81e3bcf2
- Add memory settings for hs_metrics and multiple_metrics · aebad7df
  van den Berg authored Jul 28, 2020
  
  aebad7df
- Make sure female-threshold is a float · e2c4274e
  van den Berg authored Jul 28, 2020
  
  e2c4274e
- Merge branch 'devel' of git.lumc.nl:klinische-genetica/capture-lumc/hutspot into devel · 6ec83a6b
  van den Berg authored Jul 28, 2020
  
  6ec83a6b
- Add slurm cluster configuration · 0c208c5d
  van den Berg authored Jul 28, 2020
  
  0c208c5d