Commits · master · Gonzalo S Nido / wgbs-pipeline

18 Sep, 2020 5 commits
- Added trimmomatic installation · b44f46f5
  Gonzalo S Nido authored Sep 18, 2020
  
  b44f46f5
- Added Java installation · ce340269
  Gonzalo S Nido authored Sep 18, 2020
  
  ce340269
- Merge branch 'master' of https://git.app.uib.no/gni042/wgbs-pipeline · dc430961
  Gonzalo S Nido authored Sep 18, 2020
  
  dc430961
- Individual tasks script · afe2587a
  Gonzalo S Nido authored Sep 18, 2020
  
  afe2587a
- Update prepare_vm.sh with installation of FastQC · 89a7a45f
  Gonzalo S Nido authored Sep 18, 2020
  
  89a7a45f
11 Sep, 2020 1 commit
- Added -f to pigz · 7ef42c14
  Gonzalo S Nido authored Sep 11, 2020
  
  7ef42c14
09 Sep, 2020 2 commits
- Fixed absolute path · c61a9725
  Gonzalo S Nido authored Sep 09, 2020
  
  c61a9725
- Increased fileshare size and separated strategies · 8cab38ea
  Gonzalo S Nido authored Sep 09, 2020
  
  8cab38ea
08 Sep, 2020 1 commit
- Added resizing of small results file share · 5b6a62a5
  Gonzalo S Nido authored Sep 08, 2020
  
  5b6a62a5
07 Sep, 2020 1 commit
- Important updates (Closes #1 ) · f1f7fb04
  Gonzalo S Nido authored Sep 07, 2020
  
  f1f7fb04
06 Sep, 2020 1 commit
- Update process_by_sampleid.sh · 60eb9f6f
  Gonzalo S Nido authored Sep 06, 2020
  
  60eb9f6f
04 Sep, 2020 6 commits
- Changed Lambda chr name to agree with Encode downloaded reference · 3dbf7004
  Gonzalo S Nido authored Sep 04, 2020
  
  3dbf7004
- Update wgbs-pipeline.sh · 3e37d5d1
  Gonzalo S Nido authored Sep 04, 2020
  
  3e37d5d1
- Update prepare_vm.sh · 47f189f5
  Gonzalo S Nido authored Sep 04, 2020
  
  47f189f5
- Merge branch 'scp-sample' into 'master' · d22e6824
  Gonzalo S Nido authored Sep 04, 2020
```
First ready-to-use Azure version

See merge request !1
```
  d22e6824
- Merge branch 'master' into 'scp-sample' · 84b7d4a3
  Gonzalo S Nido authored Sep 04, 2020
```
# Conflicts:
#   prepare_vm.sh
```
  84b7d4a3
- First ready-to-use Azure version · 0a35040a
  Gonzalo S Nido authored Sep 04, 2020
  
  0a35040a
01 Sep, 2020 1 commit
- Update generate_bs_indices.sh · 10abca86
  Gonzalo S Nido authored Sep 01, 2020
  
  10abca86
27 Aug, 2020 1 commit
- Delete non-deduplicated bam file to save tons of space · 7ab4ed09
  Gonzalo S Nido authored Aug 27, 2020
  
  7ab4ed09
25 Aug, 2020 3 commits
- Added pigz instead of gzip · f91f0e2d
  Gonzalo S Nido authored Aug 25, 2020
  
  f91f0e2d
- Quick fix · 5d46a9f4
  Gonzalo S Nido authored Aug 25, 2020
  
  5d46a9f4
- Fixed Lambda chromosome name and added test · 22296bd9
  Gonzalo S Nido authored Aug 25, 2020
  
  22296bd9
20 Aug, 2020 1 commit
- Pulled from origin and merged conflicts · aac44737
  Gonzalo S Nido authored Aug 20, 2020
  
  aac44737
19 Aug, 2020 3 commits
- Fixed some bugs · cae1d186
  Gonzalo S Nido authored Aug 19, 2020
  
  cae1d186
- Changed samtools merge for cat in all calls · 350d3590
  Gonzalo S Nido authored Aug 19, 2020
  
  350d3590
- Fixed number of cores for alignment based on RAM · 6c0dd0ab
  Gonzalo S Nido authored Aug 19, 2020
  
  6c0dd0ab
18 Aug, 2020 1 commit
- Some unknown changes that I probably don't need · eb057860
  Gonzalo S Nido authored Aug 18, 2020
  
  eb057860
17 Aug, 2020 2 commits
- typo · c515c520
  Gonzalo S Nido authored Aug 17, 2020
  
  c515c520
- cat instead of merge · f107c8e9
  Gonzalo S Nido authored Aug 17, 2020
  
  f107c8e9
07 Aug, 2020 6 commits
- Bug fix · abca2299
  Gonzalo S Nido authored Aug 07, 2020
  
  abca2299
- Fixed some bugs and tested the monitoring · 4123e0f2
  Gonzalo S Nido authored Aug 07, 2020
  
  4123e0f2
- Aaaand another small change · 32e21880
  Gonzalo S Nido authored Aug 07, 2020
  
  32e21880
- Yet another mistake · 39dc104d
  Gonzalo S Nido authored Aug 07, 2020
  
  39dc104d
- Stupid mistake fixed · f309da16
  Gonzalo S Nido authored Aug 07, 2020
  
  f309da16
- Some small changes · 761a693e
  Gonzalo S Nido authored Aug 07, 2020
  
  761a693e
06 Aug, 2020 4 commits
- Minor cosmetic fixes · b16035ec
  Gonzalo S Nido authored Aug 06, 2020
  
  b16035ec
- Changed lambda chr name, added automatic reference donwload/build · d1ae404e
  Gonzalo S Nido authored Aug 06, 2020
  
  d1ae404e
- Added tmp directory for Bismark alignments · dc255d67
  Gonzalo S Nido authored Aug 06, 2020
  
  dc255d67
- Added CPU/RAM monitoring, but UNTESTED · 7825a455
  Gonzalo S Nido authored Aug 06, 2020
  
  7825a455
05 Aug, 2020 1 commit
- Fixed the subset of reads in aln · a0b4bd07
  Gonzalo S Nido authored Aug 05, 2020
  
  a0b4bd07