Diffusion eSCT pipeline interoperability 03d1a3713b79

Adding MelArray repository
03d1a3713b79
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Authored by laurenczy on May 7 2018, 12:51.

Description

Adding MelArray repository

Details

Committed

laurenczy

May 7 2018, 12:51

Pushed

laurenczy

May 7 2018, 12:51

Parents

R2915:3279c9f29cb2: Dry-run functionality

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Event Timeline

laurenczy committed R2915:03d1a3713b79: Adding MelArray repository (authored by laurenczy).May 7 2018, 12:51

Changes (39)

		Path
A	(dir)	SIS/MelArray/
A		SIS/MelArray/README.md
A		SIS/MelArray/Snakefile
A		SIS/MelArray/create_validation.sh
A	(dir)	SIS/MelArray/data/
A	(dir)	SIS/MelArray/data/extra_files/
P		SIS/MelArray/data/extra_files/put_here_the_bed_and_tumor_normal_and_interval_files Copied from UniBe/hello_world_pipeline/data/.snakemake/input_tracking/b3V0cHV0L2hlbGxvXzAubG9n
A	(dir)	SIS/MelArray/pipeline/
A	(dir)	SIS/MelArray/pipeline/configs/
A		SIS/MelArray/pipeline/configs/config.yaml
A		SIS/MelArray/pipeline/configs/config_enhancer.yaml
A		SIS/MelArray/pipeline/configs/melarray_deploy_enhancer_SGE.yaml
A		SIS/MelArray/pipeline/configs/melarray_deploy_enhancer_lsf.yaml
A	(dir)	SIS/MelArray/pipeline/scripts/
A		SIS/MelArray/pipeline/scripts/get_tumor_normal_dict.py
A		SIS/MelArray/pipeline/scripts/load_config.py
A		SIS/MelArray/pipeline/scripts/overwrite_config.py
A		SIS/MelArray/pipeline/scripts/parse_ids.py
A		SIS/MelArray/pipeline/scripts/replace_in_config.py
A	(dir)	SIS/MelArray/pipeline/subworkflows/
A		SIS/MelArray/pipeline/subworkflows/AnaCovar.snake
A		SIS/MelArray/pipeline/subworkflows/Fusion.snake
A		SIS/MelArray/pipeline/subworkflows/GATK.snake
A		SIS/MelArray/pipeline/subworkflows/HaploCaller.snake
A		SIS/MelArray/pipeline/subworkflows/Mixcr.snake
A		SIS/MelArray/pipeline/subworkflows/OptiType.snake
A		SIS/MelArray/pipeline/subworkflows/QC.snake
A		SIS/MelArray/pipeline/subworkflows/Sequenza.snake
A		SIS/MelArray/pipeline/subworkflows/TrimAlign.snake
A		SIS/MelArray/pipeline/subworkflows/VariantAnnotation.snake
A		SIS/MelArray/pipeline/subworkflows/VariantCaller.snake
A	(dir)	SIS/MelArray/ref/
A	(dir)	SIS/MelArray/ref/hg19/
P		SIS/MelArray/ref/hg19/put_here_the_reference_files Copied from UniBe/hello_world_pipeline/data/.snakemake/input_tracking/b3V0cHV0L2hlbGxvXzAubG9n
A	(dir)	SIS/MelArray/ref/hg38/
P		SIS/MelArray/ref/hg38/put_here_the_reference_files Copied from UniBe/hello_world_pipeline/data/.snakemake/input_tracking/b3V0cHV0L2hlbGxvXzAubG9n
A		SIS/MelArray/ref_validation.md5
A		SIS/MelArray/run_SGE.sh
A		SIS/MelArray/run_lsf.sh