Resolve "Add mapping and trimming" (!5) · Merge requests · BICF / Astrocyte / chipseq_analysis

Merged Resolve "Add mapping and trimming"

3-mapping-trimming into master

Merged Venkat Malladi requested to merge 3-mapping-trimming into master 7 years ago

Oct 09, 2017
- 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
- 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

Resolve "Add mapping and trimming"

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