Commits · 2fb3b9f01c84909913f41306c0e475acb92b3f5e · Klinische Genetica / capture-lumc / hutspot · GitLab

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Apr 21, 2020
- Remove unneeded scripts, rules and containers · 2fb3b9f0
  van den Berg authored Apr 21, 2020
  
  2fb3b9f0
- Remove code to calculate vcf stats · cfd0cdac
  van den Berg authored Apr 21, 2020
  
  cfd0cdac
- Fix tests, remove vcf statistics from stats file · d51305c4
  van den Berg authored Apr 21, 2020
  
  d51305c4
- Integrate cutadapt summary in stats.tsv · f5032967
  van den Berg authored Apr 21, 2020
  
  f5032967
Apr 20, 2020
- Add detailed metrics output to test · 00ee0dcd
  van den Berg authored Apr 20, 2020
  
  00ee0dcd
- Add tests for two samples · 8fa81b5f
  van den Berg authored Apr 20, 2020
  
  8fa81b5f
- Add metrics to default output · bd0401ed
  van den Berg authored Apr 20, 2020
  
  bd0401ed
- Add collect metrics script · 97809466
  van den Berg authored Apr 20, 2020
  97809466
- Update multiqc, add logfile to cutadapt · fcfa28c2
  van den Berg authored Apr 20, 2020
  
  fcfa28c2
Apr 18, 2020
- Add summary output for cutadapt · b8934d0a
  van den Berg authored Apr 18, 2020
  b8934d0a
- No longer merge fastq files · 8670b32a
  van den Berg authored Apr 18, 2020
  8670b32a
Apr 17, 2020
- Create bamfile, fastq statistics disabled · fe901858
  van den Berg authored Apr 17, 2020
  
  fe901858
- Reorganise the test data, add readgroups test · c5677473
  van den Berg authored Apr 17, 2020
  
  c5677473
Apr 16, 2020
- Update graph · 6475508a
  van den Berg authored Apr 16, 2020
  
  6475508a
- Update readme and example configuration files · 47300737
  van den Berg authored Apr 16, 2020
  
  47300737
- Merge branch 'gvcf-bin' into devel · 225f4488
  van den Berg authored Apr 16, 2020
  
  225f4488
- Add tests for multiple known site vcf files · a5195446
  van den Berg authored Apr 16, 2020
  
  a5195446
- Add tests for bedfile · 14ce6cb4
  van den Berg authored Apr 16, 2020
  
  14ce6cb4
- Move refflat results to the coverage folder · 0102bc14
  van den Berg authored Apr 16, 2020
  
  0102bc14
- Add tests for refFlat file · 54377996
  van den Berg authored Apr 16, 2020
  
  54377996
Apr 15, 2020
- Remove global python variables · 7da15fdb
  van den Berg authored Apr 15, 2020
  7da15fdb
Apr 08, 2020
- Add the vcf index (tbi) to the pipeline output · 7fc6f06e
  van den Berg authored Apr 8, 2020
  
  7fc6f06e
Apr 07, 2020
- Mark the scattered vcf outputs as temporary · 1bac00d0
  van den Berg authored Apr 7, 2020
  
  1bac00d0
- Add constant GVCF bands with 20GQ increments · 6e3205d1
  van den Berg authored Apr 7, 2020
  6e3205d1
Apr 06, 2020
- Add a parameter for SCATTER_SIZE · 74dd7e6c
  van den Berg authored Apr 6, 2020
  74dd7e6c
- Add g.vcf file to default output of the pipeline · bcd99d28
  van den Berg authored Apr 6, 2020
  bcd99d28
Apr 03, 2020
- Increase scatter size to 1 billion · 2d7fe358
  van den Berg authored Apr 3, 2020
  
  2d7fe358
- Merge scattered vcf files with checkpoint · 77fe9854
  van den Berg authored Apr 3, 2020
  77fe9854
Apr 01, 2020
- Add different chunk to expected output · 3f1e4cf8
  van den Berg authored Apr 1, 2020
  
  3f1e4cf8
Mar 31, 2020
- Add input constraint · 84e685d4
  van den Berg authored Mar 31, 2020
  
  84e685d4
- Switch to using snakemake checkpoints · 745aff96
  van den Berg authored Mar 31, 2020
  
  745aff96
- WIP: move to single sample calling · 57eaea50
  van den Berg authored Mar 31, 2020
  
  57eaea50
- Make the scatter output dynamic · e7a546d4
  van den Berg authored Mar 31, 2020
  e7a546d4
- Add biopet scatter · f0e48bfc
  van den Berg authored Mar 31, 2020
  
  f0e48bfc
Mar 30, 2020
- Add dictionary for singularity containers · 26049506
  van den Berg authored Mar 30, 2020
  
  26049506
- Add specific tests for content vcf file · 29cc1c8c
  van den Berg authored Mar 30, 2020
  
  29cc1c8c
- Update requirements due to conda dependency error · 7a6274f5
  van den Berg authored Mar 30, 2020
  
  7a6274f5
Jan 14, 2020
- Use local tmp folder as java tempdir · 3c5edeb2
  van den Berg authored Jan 14, 2020
  3c5edeb2
Jan 13, 2020
- Deprecate fastq_count · 1155ac47
  van den Berg authored Jan 13, 2020
  
  1155ac47
Jan 10, 2020
- Merge branch 'known-snps' into 'master' · 6b99e0eb
  van den Berg authored Jan 10, 2020
  6b99e0eb