Commits · cc0b8e0590891e583aaf10fb77c46d0bfcc31e7c · BICF / Astrocyte / chipseq_analysis

Oct 08, 2017
- 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
- Add in trace config and fix varaible of map_reads. · 0205044c
  Venkat Malladi authored 7 years ago
  
  0205044c
- Fix file used in first step. · 08898dde
  Venkat Malladi authored 7 years ago
  
  08898dde
- Fix missing libraries and use of python3. · 861b7993
  Venkat Malladi authored 7 years ago
  
  861b7993
Oct 05, 2017
- Rename config file. · 758cf363
  Venkat Malladi authored 7 years ago
  
  758cf363
- Add in maping step with apporpriate configurations. · 14299993
  Venkat Malladi authored 7 years ago
  
  14299993
Oct 04, 2017
- Add in nextflow config for loading modules. · 38f026a1
  Venkat Malladi authored 7 years ago
  
  38f026a1
Oct 03, 2017
- Consistency in documentation. · 932baa0d
  Venkat Malladi authored 7 years ago
  
  932baa0d
- Update trim_reads to extrapolate the params. · 13fe4335
  Venkat Malladi authored 7 years ago
  
  13fe4335
- Update trim command name. · fd33ecb7
  Venkat Malladi authored 7 years ago
  
  fd33ecb7
- Add in trimming step into workflow. · f3c034a7
  Venkat Malladi authored 7 years ago
  
  f3c034a7
- Add in argument for trim_parameters. · 5532fa6d
  Venkat Malladi authored 7 years ago
  
  5532fa6d
- update path variables in logger output · b583f9b0
  Venkat Malladi authored 7 years ago
  
  b583f9b0
- update path variables · 31ffef27
  Venkat Malladi authored 7 years ago
  
  31ffef27
- Fix logger syntax. · 4b135733
  Venkat Malladi authored 7 years ago
  
  4b135733
Oct 01, 2017
- Add triming of reads, remove fastqc step. · 84872f97
  Venkat Malladi authored 7 years ago
  
  84872f97
Sep 30, 2017
- Merge branch '1-fastqc' into 'master' · c9f0a2c4
  Venkat Malladi authored 7 years ago
```
Resolve "Add in Fastqc"

Closes #1

See merge request !4
```
  c9f0a2c4
- Merge branch 'master' into '1-fastqc' · cb70f489
  Venkat Malladi authored 7 years ago
```
# Conflicts:
#   .gitlab-ci.yml
```
  cb70f489
- Add in fastqc step. · 3d73714a
  Venkat Malladi authored 7 years ago
  
  3d73714a
Sep 28, 2017
- Pass nextflow test for design file. · 8ef6e674
  Venkat Malladi authored 7 years ago
  
  8ef6e674
Sep 27, 2017
- Remove directory change. · ee536623
  Venkat Malladi authored 7 years ago
  
  ee536623
- Add information for local library. · eb8f7642
  Venkat Malladi authored 7 years ago
  
  eb8f7642
- Add in pytest-pythonpath. · 46d64cf6
  Venkat Malladi authored 7 years ago
  
  46d64cf6
- Add in dummy gitlab file. · 2728fc7e
  Venkat Malladi authored 7 years ago
  
  2728fc7e
Sep 26, 2017
- Update gitlab ci for pytest. · b3322653
  Venkat Malladi authored 7 years ago
  
  b3322653
- Add in test for design files. · 02bef1b4
  Venkat Malladi authored 7 years ago
  
  02bef1b4