Split into files ; define modes & associated conda envs ; run on a single...
Split into files ; define modes & associated conda envs ; run on a single chromosome by keeping full initial BAM ; functionnal until strandphaser
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- workflow/report.html 3145 additions, 0 deletionsworkflow/report.html
- workflow/report/custom-stylesheet.css 9 additions, 0 deletionsworkflow/report/custom-stylesheet.css
- workflow/report/mosaic_counts.rst 1 addition, 0 deletionsworkflow/report/mosaic_counts.rst
- workflow/report/workflow.rst 1 addition, 0 deletionsworkflow/report/workflow.rst
- workflow/rules/count.smk 180 additions, 0 deletionsworkflow/rules/count.smk
- workflow/rules/input_check.smk 16 additions, 0 deletionsworkflow/rules/input_check.smk
- workflow/rules/plots.smk 109 additions, 0 deletionsworkflow/rules/plots.smk
- workflow/rules/regenotyping.smk 66 additions, 0 deletionsworkflow/rules/regenotyping.smk
- workflow/rules/segmentation.smk 136 additions, 0 deletionsworkflow/rules/segmentation.smk
- workflow/rules/strandphaser.smk 183 additions, 0 deletionsworkflow/rules/strandphaser.smk
- workflow/rules/utils.smk 70 additions, 0 deletionsworkflow/rules/utils.smk
- workflow/scripts/__pycache__/handle_input.cpython-38.pyc 0 additions, 0 deletionsworkflow/scripts/__pycache__/handle_input.cpython-38.pyc
- workflow/scripts/plotting/qc.R 366 additions, 0 deletionsworkflow/scripts/plotting/qc.R
- workflow/scripts/segmentation_scripts/detect_strand_states.py 460 additions, 0 deletions...flow/scripts/segmentation_scripts/detect_strand_states.py
- workflow/scripts/segmentation_scripts/fix_segmentation.awk 8 additions, 0 deletionsworkflow/scripts/segmentation_scripts/fix_segmentation.awk
- workflow/scripts/strandphaser_scripts/StrandPhaseR_pipeline.R 16 additions, 0 deletions...flow/scripts/strandphaser_scripts/StrandPhaseR_pipeline.R
- workflow/scripts/strandphaser_scripts/helper.convert_strandphaser_input.R 10 additions, 0 deletions.../strandphaser_scripts/helper.convert_strandphaser_input.R
- workflow/scripts/strandphaser_scripts/helper.convert_strandphaser_output.R 30 additions, 0 deletions...strandphaser_scripts/helper.convert_strandphaser_output.R
- workflow/scripts/strandphaser_scripts/install_strandphaser.R 47 additions, 0 deletionsworkflow/scripts/strandphaser_scripts/install_strandphaser.R
- workflow/scripts/utils/generate_exclude_file.py 18 additions, 0 deletionsworkflow/scripts/utils/generate_exclude_file.py
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