Commits · 33faba145f15e15208c2b48c77647f4b6726c6e7 · Klinische Genetica / capture-lumc / hutspot · GitLab

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May 29, 2020
- Add picard multiple metrics · 33faba14
  van den Berg authored May 29, 2020
  33faba14
- Enable json output for multiqc · 067315ba
  van den Berg authored May 29, 2020
  
  067315ba
- Update pytest-workflow requirement · dad3bdcb
  van den Berg authored May 29, 2020
  
  dad3bdcb
- Merge branch 'devel' of https://git.lumc.nl/klinische-genetica/capture-lumc/hutspot into devel · 573858c6
  van den Berg authored May 29, 2020
  
  573858c6
- Add test for raw bases and reads · 9c319c5c
  van den Berg authored May 29, 2020
  9c319c5c
May 01, 2020
- Increase memory for covstats · 842a5329
  van den Berg authored May 1, 2020
  
  842a5329
Apr 30, 2020
- Increase scatterregion memory limit · ae8ea7e5
  van den Berg authored Apr 30, 2020
  
  ae8ea7e5
- Add memory requirement to scatterregions · 60fd2489
  van den Berg authored Apr 30, 2020
  
  60fd2489
- Make sure relative paths are handled properly · 708669a1
  van den Berg authored Apr 30, 2020
  
  708669a1
- Rename libraries in config to read_groups · 0d2a8c03
  van den Berg authored Apr 30, 2020
  0d2a8c03
Apr 29, 2020
- Clean up coverage stats header names · b89b3b6e
  van den Berg authored Apr 29, 2020
  
  b89b3b6e
- Switch to using a --configfile · 4a3483a7
  van den Berg authored Apr 29, 2020
  
  4a3483a7
Apr 23, 2020
- Merge branch 'no-merge' into 'devel' · 326944a8
  van den Berg authored Apr 23, 2020
  326944a8
- use plain pytest · ec08fd25
  Ruben Vorderman authored Apr 23, 2020
  
  ec08fd25
- update singularity image · dfc4966e
  Ruben Vorderman authored Apr 23, 2020
  
  dfc4966e
- Add workflow-threads to speed up the tests · ae0cb74d
  van den Berg authored Apr 23, 2020
  
  ae0cb74d
- Remove debugging and enable all tests for gitlab-ci · 85a500c7
  van den Berg authored Apr 23, 2020
  
  85a500c7
Apr 22, 2020
- try multiple attempts to get status · eed3123d
  Ruben Vorderman authored Apr 22, 2020
  
  eed3123d
- Revert "use clone git strategy" · 9f4af101
  Ruben Vorderman authored Apr 22, 2020
  9f4af101
- Show sacct -j output on status parsing failure · 579ce3c8
  Ruben Vorderman authored Apr 22, 2020
  
  579ce3c8
- use clone git strategy · a42d185f
  Ruben Vorderman authored Apr 22, 2020
  
  a42d185f
- Use consistent flags for sbatch · ed02faec
  van den Berg authored Apr 22, 2020
  
  ed02faec
- Update slurm-cluster-status · 361fff51
  van den Berg authored Apr 22, 2020
  
  361fff51
- Put shebang in custom script. · dd7f27aa
  Ruben Vorderman authored Apr 22, 2020
  
  dd7f27aa
- Merge branch 'BQSR' into no-merge · 6ae51efb
  van den Berg authored Apr 22, 2020
  
  6ae51efb
- Call GATK baserecalibrate on readgroup bam files · e5d36df3
  van den Berg authored Apr 22, 2020
  e5d36df3
- Use pwd for current folder in PATH · 71462a00
  van den Berg authored Apr 22, 2020
  
  71462a00
- Drop the bash PATH cache · 40638d2b
  van den Berg authored Apr 22, 2020
  
  40638d2b
Apr 21, 2020
- Inject slurm submission into integration test · 7ac07858
  van den Berg authored Apr 21, 2020
  
  7ac07858
- Use environment conda to run integration · d6880eee
  van den Berg authored Apr 21, 2020
  
  d6880eee
- Try using pip for slurm runner · 2a54274e
  van den Berg authored Apr 21, 2020
  
  2a54274e
- Remove docker image from slurm runner · e12cbb90
  van den Berg authored Apr 21, 2020
  
  e12cbb90
- Add singularity anchor · 5c395116
  van den Berg authored Apr 21, 2020
  
  5c395116
- set BASETEMP and remove functional tag · dfb090d0
  van den Berg authored Apr 21, 2020
  
  dfb090d0
- Update gitlab-ci tests · 13104ddf
  van den Berg authored Apr 21, 2020
  
  13104ddf
- 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