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Snakefile
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configfile:
"snakemake_config.yml"
workdir:
config['workdir']
smkdir = config['codedir']+"/snakemake/"
include:
smkdir+"downloaded_data_parse.smk"
include:
smkdir+"model_validation.smk"
include:
smkdir+"frequency_analysis.smk"
include:
smkdir+"nanonome_data_parse.smk"
include:
smkdir+"sv_analysis.smk"
samples_tb = pd.read_csv(config['codedir']+"/sample_info.csv")
rule parse_downloaded_data:
input:
"data/gm12878/GM12878_CTCF.noTSS.center.2000bp.bed",
"data/hg38/hg38_genes.TSS.slop2000bp.bed",
"data/hg38/hg38_cgi.bed"
rule model_validation:
input:
"plots/NA12878_ROC_CpG_methylation_cpg_model.pdf",
"plots/NA12878_ROC_GpC_methylation_gpc_model.pdf"
rule frequency_analysis:
input:
"plots/GM12878_nanoNOMe.pooled.metaplot.CTCF.noTSS.center.2000bp.pdf",
"plots/GM12878_BSseq.metaplot.CTCF.noTSS.center.2000bp.pdf",
"plots/GM12878_MNase.metaplot.CTCF.noTSS.center.2000bp.pdf"
rule nanonome_data:
input:
expand("analysis/mbed/{sample}.{mod}.meth.bed.gz",
sample=samples_tb['sample'],
mod=["cpg","gpc"])
rule sv_analysis:
input:
expand("data/bcan/MCF10A_vs_{sample}_SVcomparison_{svtype}_survivor.flank200bp.bed",
sample=["MCF7","MDAMB231"],
svtype=["del","ins"]),
expand("data/bcan/MCF10A_vs_{sample}_SVcomparison_{svtype}_survivor.shuffle.flank200bp.bed",
sample=["MCF7","MDAMB231"],
svtype=["del","ins"]),
expand("data/bcan/MCF10A_vs_{sample}_SVcomparison_tra_survivor.TRAregion200bp.bed",
sample=["MCF7","MDAMB231"]),
expand("data/bcan/MCF10A_vs_{sample}_SVcomparison_tra_survivor.shuffle.TRAregion200bp.bed",
sample=["MCF7","MDAMB231"])