Commits · c41e1217cd0cf26caa2bd45884af2342f06438cf · BICF / Astrocyte / chipseq_analysis

Oct 10, 2017
- Fix outputs. · c41e1217
  Venkat Malladi authored 7 years ago
  
  c41e1217
- Update paths and add in testing if file exists. · d7b9a6ba
  Venkat Malladi authored 7 years ago
  
  d7b9a6ba
- Fix spacing. · cb8162c6
  Venkat Malladi authored 7 years ago
  
  cb8162c6
- Update triming to have generalized paths. · d6a5bea0
  Venkat Malladi authored 7 years ago
  
  d6a5bea0
- Add header to pbc file. · 9b65c0bd
  Venkat Malladi authored 7 years ago
  
  9b65c0bd
- Update samtools version and synxtax to fix bugs in last push. · 2948ddca
  Venkat Malladi authored 7 years ago
  
  2948ddca
Oct 09, 2017
- Fix syntax to be tsv format. · ea8a20e5
  Venkat Malladi authored 7 years ago
  
  ea8a20e5
- Remove resume as it is ignored. · de6185ea
  Venkat Malladi authored 7 years ago
  
  de6185ea
- Add in option for resume. · 5ac11bb7
  Venkat Malladi authored 7 years ago
  
  5ac11bb7
- Fix option. · 2c4516e9
  Venkat Malladi authored 7 years ago
  
  2c4516e9
- Update incorrect line break. · adf18e06
  Venkat Malladi authored 7 years ago
  
  adf18e06
- update output. · 7d54e3fe
  Venkat Malladi authored 7 years ago
  
  7d54e3fe
- Add in steps to remove dups and filter reads. · 3a9a868b
  Venkat Malladi authored 7 years ago
  
  3a9a868b
- Merge branch '3-mapping-trimming' into 'master' · 4357eb15
  Venkat Malladi authored 7 years ago
```
Resolve "Add mapping and trimming"

Closes #3

See merge request !5
```
  4357eb15
- Update testing params. · 034d2f58
  Venkat Malladi authored 7 years ago
  
  034d2f58
- update path to trim file. · 99436c11
  Venkat Malladi authored 7 years ago
  
  99436c11
- Update file collection. · 9acca710
  Venkat Malladi authored 7 years ago
  
  9acca710
- Update path to files to pass tests. · a39198b6
  Venkat Malladi authored 7 years ago
  
  a39198b6
Oct 08, 2017
- Add in test for testing map reads singleend. · d8c9c53b
  Venkat Malladi authored 7 years ago
  
  d8c9c53b
- Fix syntax. · de0f2837
  Venkat Malladi authored 7 years ago
  
  de0f2837
- Add in test for verifying single end trim reads. · f0fbf42b
  Venkat Malladi authored 7 years ago
  
  f0fbf42b
- Change genome to GRCm38 to reflect data. · b59f7e0c
  Venkat Malladi authored 7 years ago
  
  b59f7e0c
- Cleanup code after flake8. · daaf631d
  Venkat Malladi authored 7 years ago
  
  daaf631d
- collect the qc metrics. · a33eb4d4
  Venkat Malladi authored 7 years ago
  
  a33eb4d4
- Add in place holders for testing trim reads. · fe645c1a
  Venkat Malladi authored 7 years ago
  
  fe645c1a
- generatlized strip_extension and added tests. · cc0b8e05
  Venkat Malladi authored 7 years ago
  
  cc0b8e05
- Add in test for utils. · 6b2c56dc
  Venkat Malladi authored 7 years ago
  
  6b2c56dc
- Remove memory constraints. · 577d7b85
  Venkat Malladi authored 7 years ago
  
  577d7b85
- Fix bwa aln variables. · 34f899e0
  Venkat Malladi authored 7 years ago
  
  34f899e0
- Fix bam syntax and file name. · c7af593e
  Venkat Malladi authored 7 years ago
  
  c7af593e
Oct 07, 2017
- Fix the output directory name. · e38a082d
  Venkat Malladi authored 7 years ago
  
  e38a082d
- Fix version of bwa · d8c5f740
  Venkat Malladi authored 7 years ago
  
  d8c5f740
- Fix order of sai and fastq arguments. · 1b918e88
  Venkat Malladi authored 7 years ago
  
  1b918e88
- update the naming of the reads. · 3d77cb5b
  Venkat Malladi authored 7 years ago
  
  3d77cb5b
- Update bwa version to match index. · d14969c6
  Venkat Malladi authored 7 years ago
  
  d14969c6
- Add in nextflow test. · d9572f4c
  Venkat Malladi authored 7 years ago
  
  d9572f4c
- update samtools flagstat and name of outfile · 2e634083
  Venkat Malladi authored 7 years ago
  
  2e634083
Oct 06, 2017
- Fix missing variable and naming conventions. · 6a389e7f
  Venkat Malladi authored 7 years ago
  
  6a389e7f
- Fix astrocyte_pkg.yml · 2bd72c5d
  Venkat Malladi authored 7 years ago
  
  2bd72c5d
- Use python3 for testing the design file and use local for this. · 970fea4b
  Venkat Malladi authored 7 years ago
  
  970fea4b