Diffusion eSCT pipeline interoperability 88e9313e0804

Adding MelArray to public branch
88e9313e0804
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Authored by laurenczy on May 7 2018, 14:15.

Description

Adding MelArray to public branch

Details

Committed

laurenczy

May 7 2018, 14:15

Pushed

laurenczy

May 7 2018, 14:15

Parents

R2915:dd9118611f13: Added guidelines PDF

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Unknown

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Event Timeline

laurenczy committed R2915:88e9313e0804: Adding MelArray to public branch (authored by laurenczy).May 7 2018, 14:15

Changes (44)

		Path
A	(dir)	example_pipelines/MelArray/
A		example_pipelines/MelArray/README.md
A		example_pipelines/MelArray/Snakefile
A		example_pipelines/MelArray/create_validation.sh
A	(dir)	example_pipelines/MelArray/data/
A	(dir)	example_pipelines/MelArray/data/extra_files/
A		example_pipelines/MelArray/data/extra_files/put_here_the_bed_and_tumor_normal_and_interval_files
A	(dir)	example_pipelines/MelArray/other/
A	(dir)	example_pipelines/MelArray/other/enhancer_png/
A		example_pipelines/MelArray/other/enhancer_png/melarray_v5p2_dag_sub_hori.png
A		example_pipelines/MelArray/other/enhancer_png/melarray_v5p2_rulegraph_all_hori_marked.png
A		example_pipelines/MelArray/other/enhancer_png/melarray_v5p2_rulegraph_sub_hori.png
A	(dir)	example_pipelines/MelArray/pipeline/
A	(dir)	example_pipelines/MelArray/pipeline/configs/
A		example_pipelines/MelArray/pipeline/configs/config.yaml
A		example_pipelines/MelArray/pipeline/configs/config_enhancer.yaml
A		example_pipelines/MelArray/pipeline/configs/melarray_deploy_enhancer_SGE.yaml
A		example_pipelines/MelArray/pipeline/configs/melarray_deploy_enhancer_lsf.yaml
A	(dir)	example_pipelines/MelArray/pipeline/scripts/
A		example_pipelines/MelArray/pipeline/scripts/get_tumor_normal_dict.py
A		example_pipelines/MelArray/pipeline/scripts/load_config.py
A		example_pipelines/MelArray/pipeline/scripts/overwrite_config.py
A		example_pipelines/MelArray/pipeline/scripts/parse_ids.py
A		example_pipelines/MelArray/pipeline/scripts/replace_in_config.py
A	(dir)	example_pipelines/MelArray/pipeline/subworkflows/
A		example_pipelines/MelArray/pipeline/subworkflows/AnaCovar.snake
A		example_pipelines/MelArray/pipeline/subworkflows/Fusion.snake
A		example_pipelines/MelArray/pipeline/subworkflows/GATK.snake
A		example_pipelines/MelArray/pipeline/subworkflows/HaploCaller.snake
A		example_pipelines/MelArray/pipeline/subworkflows/Mixcr.snake
A		example_pipelines/MelArray/pipeline/subworkflows/OptiType.snake
A		example_pipelines/MelArray/pipeline/subworkflows/QC.snake
A		example_pipelines/MelArray/pipeline/subworkflows/Sequenza.snake
A		example_pipelines/MelArray/pipeline/subworkflows/TrimAlign.snake
A		example_pipelines/MelArray/pipeline/subworkflows/VariantAnnotation.snake
A		example_pipelines/MelArray/pipeline/subworkflows/VariantCaller.snake
A	(dir)	example_pipelines/MelArray/ref/
A	(dir)	example_pipelines/MelArray/ref/hg19/
A		example_pipelines/MelArray/ref/hg19/put_here_the_reference_files
A	(dir)	example_pipelines/MelArray/ref/hg38/
A		example_pipelines/MelArray/ref/hg38/put_here_the_reference_files
A		example_pipelines/MelArray/ref_validation.md5
A		example_pipelines/MelArray/run_SGE.sh
A		example_pipelines/MelArray/run_lsf.sh