Commits · 524d34af8b1aab882a13313c5519818d13711a3f · Klinische Genetica / capture-lumc / hutspot

08 May, 2019 9 commits
- python3-pip · 524d34af
  Sander Bollen authored May 08, 2019
  
  524d34af
- pip3 · 833869cc
  Sander Bollen authored May 08, 2019
  
  833869cc
- python3 -y · 7011f8f4
  Sander Bollen authored May 08, 2019
  
  7011f8f4
- run apt-get update · 14a41871
  Sander Bollen authored May 08, 2019
  
  14a41871
- install python · 1092c17e
  Sander Bollen authored May 08, 2019
  
  1092c17e
- forgot stage · 9f293ee8
  Sander Bollen authored May 08, 2019
  
  9f293ee8
- test singularity on CI · e351fb2d
  Sander Bollen authored May 08, 2019
  
  e351fb2d
- emulate truncate with head -c 0 · fef1b927
  Sander Bollen authored May 08, 2019
  
  fef1b927
- use unzip -l instead of unzip -t since busybox does not contain -t · 2a5d61bb
  Sander Bollen authored May 08, 2019
  
  2a5d61bb
06 May, 2019 1 commit
- add multicontainer for align rule · 2e5bee02
  Sander Bollen authored May 06, 2019
  
  2e5bee02
01 May, 2019 1 commit
- fix too many spaces · 5409bd9e
  Sander Bollen authored May 01, 2019
  
  5409bd9e
30 Apr, 2019 4 commits
- add singularity directives to some rules · 1d7a6bd9
  Sander Bollen authored Apr 30, 2019
  
  1d7a6bd9
- -T no longer exists in snakemake 5 · 7a1f120f
  Sander Bollen authored Apr 30, 2019
  
  7a1f120f
- bump snakemake version to at least 5.2.0 so we can use the "directory" · 2b1f5ca3
  Sander Bollen authored Apr 30, 2019
```
directive
```
  2b1f5ca3
- Merge pull request #3 from LUMC/java-conda · d21534e5
  Sander Bollen authored Apr 30, 2019
```
remove java dependency
```
  d21534e5
29 Apr, 2019 1 commit
- remove java dependency · e1f91027
  Sander Bollen authored Apr 29, 2019
  
  e1f91027
28 Mar, 2019 7 commits
- update submodule · 5970e699
  Sander Bollen authored Mar 28, 2019
  
  5970e699
- missing dollar sign · 6cbf1c80
  Sander Bollen authored Mar 28, 2019
  
  6cbf1c80
- add cluster status in functional test yaml · 13097276
  Sander Bollen authored Mar 28, 2019
  
  13097276
- recursive submodule strategy · 0112fcdb
  Sander Bollen authored Mar 28, 2019
  
  0112fcdb
- add slurm-cluster-status as submodule · a66ab1ee
  Sander Bollen authored Mar 28, 2019
  
  a66ab1ee
- move yaml · e2ae59f2
  Sander Bollen authored Mar 28, 2019
  
  e2ae59f2
- move sge cluster to cluster subdirectory · 5399fc25
  Sander Bollen authored Mar 28, 2019
  
  5399fc25
27 Mar, 2019 2 commits
- double quotes · a7ee85d4
  Sander Bollen authored Mar 27, 2019
  
  a7ee85d4
- use --parsable for sbatch · 75938280
  Sander Bollen authored Mar 27, 2019
  
  75938280
26 Mar, 2019 13 commits
- fix conda bin · c893a53c
  Sander Bollen authored Mar 26, 2019
  
  c893a53c
- fix gitlab ci yaml · cbe22907
  Sander Bollen authored Mar 26, 2019
  
  cbe22907
- functional test yml · 96489f04
  Sander Bollen authored Mar 26, 2019
  
  96489f04
- Merge pull request #2 from LUMC/use-builtin-output-dir · 14eed9ee
  Sander Bollen authored Mar 26, 2019
```
Use builtin output dir
```
  14eed9ee
- fix path · 2db357e3
  Sander Bollen authored Mar 26, 2019
  
  2db357e3
- keep workflow wd · 72629365
  Sander Bollen authored Mar 26, 2019
  
  72629365
- integration tests in gitlab ci · 4aa40f5c
  Sander Bollen authored Mar 26, 2019
  
  4aa40f5c
- add ref.dict to test data · 06fe1fb7
  Sander Bollen authored Mar 26, 2019
  
  06fe1fb7
- add bwa indexes for ref · 6b467c37
  Sander Bollen authored Mar 26, 2019
  
  6b467c37
- proper pairing for tests fq files · db46f2b3
  Sander Bollen authored Mar 26, 2019
  
  db46f2b3
- fix sanity checks · 74ba06c8
  Sander Bollen authored Mar 26, 2019
  
  74ba06c8
- better indentation · ad2eb71b
  Sander Bollen authored Mar 26, 2019
  
  ad2eb71b
- fix syntax errors · ef4bf0f0
  Sander Bollen authored Mar 26, 2019
  
  ef4bf0f0
21 Mar, 2019 2 commits
- use full path in softlinks in seqtk.sh · ac58a0c1
  Sander Bollen authored Mar 21, 2019
  
  ac58a0c1
- remove OUTPUT_DIR config value · 73091256
  Sander Bollen authored Mar 21, 2019
  
  73091256