Merge branch '110-SE' into 'develop'
Resolve "Change Single Read to Single End for submitted endness" Closes #95, #100, #112, #111, #70, #115, #114, and #110 See merge request !67
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- .gitlab-ci.yml 89 additions, 28 deletions.gitlab-ci.yml
- CHANGELOG.md 11 additions, 1 deletionCHANGELOG.md
- README.md 5 additions, 1 deletionREADME.md
- conftest.py 13 additions, 0 deletionsconftest.py
- docs/dag.png 0 additions, 0 deletionsdocs/dag.png
- test_data/Replicate_For_Input_Bag(test).json 2 additions, 2 deletionstest_data/Replicate_For_Input_Bag(test).json
- test_data/createTestData.sh 2 additions, 2 deletionstest_data/createTestData.sh
- workflow/conf/Replicate_For_Input_Bag.json 2 additions, 2 deletionsworkflow/conf/Replicate_For_Input_Bag.json
- workflow/conf/aws.config 3 additions, 8 deletionsworkflow/conf/aws.config
- workflow/conf/biohpc.config 3 additions, 6 deletionsworkflow/conf/biohpc.config
- workflow/nextflow.config 4 additions, 7 deletionsworkflow/nextflow.config
- workflow/rna-seq.nf 622 additions, 600 deletionsworkflow/rna-seq.nf
- workflow/scripts/parse_meta.py 3 additions, 18 deletionsworkflow/scripts/parse_meta.py
- workflow/scripts/upload_execution_run.py 0 additions, 1 deletionworkflow/scripts/upload_execution_run.py
- workflow/scripts/upload_output_bag.py 20 additions, 11 deletionsworkflow/scripts/upload_output_bag.py
- workflow/scripts/upload_qc.py 13 additions, 6 deletionsworkflow/scripts/upload_qc.py
- workflow/tests/test_alignReads.py 7 additions, 7 deletionsworkflow/tests/test_alignReads.py
- workflow/tests/test_completion.py 15 additions, 0 deletionsworkflow/tests/test_completion.py
- workflow/tests/test_dedupReads.py 9 additions, 9 deletionsworkflow/tests/test_dedupReads.py
- workflow/tests/test_makeBigWig.py 2 additions, 2 deletionsworkflow/tests/test_makeBigWig.py
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