Commits · 82cc76099e24b8b5931bb769fecbb0a0aff86fdd · biowdl / tasks

Feb 20, 2019
- Merge branch 'develop' into BIOWDL-199 · 82cc7609
  Ruben Vorderman authored 6 years ago
  
  Unverified
  
  82cc7609
- Merge pull request #89 from biowdl/BIOWDL-194 · e55fc372
  Ruben Vorderman authored 6 years ago
  
  allow for additional annotations to be added into mergecounts output
  Unverified
  
  e55fc372
- remove redundant precommand stuff · 6be49bda
  Ruben Vorderman authored 6 years ago
  
  6be49bda
- Merge branch 'develop' into BIOWDL-194 · f27a750c
  Ruben Vorderman authored 6 years ago
  
  Unverified
  
  f27a750c
- Merge pull request #91 from biowdl/BIOWDL-200 · 37442743
  Ruben Vorderman authored 6 years ago
  
  add hisat2 task
  Unverified
  
  37442743
- tabix uses its own container · d6beeeba
  Ruben Vorderman authored 6 years ago
  
  d6beeeba
- create the output dir · 3447c885
  Ruben Vorderman authored 6 years ago
  
  3447c885
- make sure scatters work correctly · 10d09e2a
  Ruben Vorderman authored 6 years ago
  
  10d09e2a
- add hisat2 task · b4f39ae6
  Cats authored 6 years ago
  
  b4f39ae6
- fix gatk images · 8479f908
  Ruben Vorderman authored 6 years ago
  
  8479f908
- fix a few things in biopet · 14eae8b4
  Ruben Vorderman authored 6 years ago
  
  14eae8b4
- fix order · 64bbcb2c
  Ruben Vorderman authored 6 years ago
  
  64bbcb2c
- scatterdir is a file · 18e19a08
  Ruben Vorderman authored 6 years ago
  
  18e19a08
- make scatterregions work in container · b7cc4761
  Ruben Vorderman authored 6 years ago
  
  b7cc4761
Feb 19, 2019
- correct name · 99767ad1
  Ruben Vorderman authored 6 years ago
  
  99767ad1
- add tags to all samtools stuff · 0e84089e
  Ruben Vorderman authored 6 years ago
  
  0e84089e
- dockerize scatterregions · c8af9b5d
  Ruben Vorderman authored 6 years ago
  
  c8af9b5d
- run python script in container · 31551e41
  Ruben Vorderman authored 6 years ago
  
  31551e41
- add docker containers to gatk · eec5791c
  Ruben Vorderman authored 6 years ago
  
  eec5791c
- Merge pull request #90 from biowdl/BIOWDL-198 · fcfe3415
  Ruben Vorderman authored 6 years ago
  
  Move all picard tasks to containers.
  Unverified
  
  fcfe3415
- add multicontainers · 8ad19fb9
  Ruben Vorderman authored 6 years ago
  
  8ad19fb9
- fix typo · 9da1cf0a
  Ruben Vorderman authored 6 years ago
  
  9da1cf0a
- remove redundant inputs · 2b183db6
  Ruben Vorderman authored 6 years ago
  
  2b183db6
- enable containers for picard · 8ec3976c
  Ruben Vorderman authored 6 years ago
  
  8ec3976c
Feb 18, 2019
- change docker tags · edfcd38d
  Cats authored 6 years ago
  
  edfcd38d
Feb 14, 2019
- add docker containers for htseq and stringtie, escape $ in mergecounts · 3f682360
  Cats authored 6 years ago
  
  3f682360
- allow for additional annotations to be added into mergecounts output · abca64c2
  Cats authored 6 years ago
  
  abca64c2
Feb 11, 2019
- Merge pull request #88 from biowdl/BIOWDL-192 · 8cad4b24
  Cats authored 6 years ago
  
  add docker for extract adapters, catadapt and fastqc
  Unverified
  
  8cad4b24
Feb 07, 2019
- add docker for extract adapters, catadapt and fastqc · 9e8bf82a
  Cats authored 6 years ago
  
  9e8bf82a
Feb 04, 2019
- Merge pull request #87 from biowdl/BIOWDL-178 · 61bdc897
  Cats authored 6 years ago
  
  Saner input for cutadapt
  Unverified
  
  61bdc897
Feb 01, 2019
- remove import from simple task · 5e23c34a
  Ruben Vorderman authored 6 years ago
  
  5e23c34a
- Merge pull request #86 from biowdl/add_docker · aa369fea
  Cats authored 6 years ago
  
  Add docker for samtools and STAR
  Unverified
  
  aa369fea
Jan 21, 2019
- add docker to other samtools tasks · c2935cd0
  Cats authored 6 years ago
  
  c2935cd0
- add docker runtime for star and samtools index · 7cdc1c77
  Cats authored 6 years ago
  
  7cdc1c77
Jan 08, 2019
- Merge pull request #85 from biowdl/PYT-8 · dd3bc65c
  Cats authored 6 years ago
  
  Make tasks suitable for running against relative paths.
  Unverified
  
  dd3bc65c
- use files not string · 1dcdf24a
  Ruben Vorderman authored 6 years ago
  
  1dcdf24a
Jan 07, 2019
- fix file · 9c2b7953
  Ruben Vorderman authored 6 years ago
  
  9c2b7953
- fix dbsnparg · c37d775c
  Ruben Vorderman authored 6 years ago
  
  c37d775c
- fix reference fasta · 998636a0
  Ruben Vorderman authored 6 years ago
  
  998636a0
- rewrite argument · e3776779
  Ruben Vorderman authored 6 years ago
  
  e3776779