removing useless rules

config/configComparison.yaml

@@ -14,6 +14,6 @@ params:
   overdispersion: none # default none, NM for overdispersion
   qValue: 0.01
   minCov: 4
-  minDiff: 0.25
+  minDiff: 25
   context: ["CpG"]
   species: "Malus"

workflow/Snakefile

@@ -5,7 +5,6 @@ include: "rules/quality.smk"
 include: "rules/genome_preparation.smk"
 include: "rules/alignment.smk"
 include: "rules/methylation_extraction.smk"
-include: "rules/methylation_calling.smk"
 
 # report template
 report: "report/workflow.rst"

workflow/rules/computeDmrs.smk

@@ -22,13 +22,8 @@ rule compute_methylkit:
 		clustersPdf=outdir+"methylation/{id}-{context}/{id}-{context}-clusters.pdf",
 		pcaScreePdf=outdir+"methylation/{id}-{context}/{id}-{context}-PCA-screeplot.pdf",
 		pcaPdf=outdir+"methylation/{id}-{context}/{id}-{context}-PCA.pdf",
-		# hyperMethylation=outdir+"methylation/{id}-{context}/{id}-{context}-HyperMethylated-stats.txt",
-		# hypoMethylation=outdir+"methylation/{id}-{context}/{id}-{context}-HypoMethylated-stats.txt",
 		overAllMethylation=outdir+"methylation/{id}-{context}/{id}-{context}-overallMethylation-stats.txt",
-		# hyperMethylationBed=outdir+"methylation/{id}-{context}/{id}-{context}-HyperMethylated.bed",
-		# hypoMethylationBed=outdir+"methylation/{id}-{context}/{id}-{context}-HypoMethylated.bed",
 		overAllMethylationBed=outdir+"methylation/{id}-{context}/{id}-{context}-overallMethylation.bed",
-		# cutoffMethylation=outdir+"methylation/{id}-{context}/{id}-{context}-cutoff.txt"
 	log:
 		outdir+"methylation/{id}-{context}/{id}-{context}-log.out"
 	conda:

workflow/rules/methylation_calling.smk

-rule read_report:
-	input:
-		get_CX_reports,
-	output:
-		rds=outdir+"results/methylation_calling/{sample}-TechRep_{techrep}/{sample}-report.rds",
-		conditionVector=outdir+"results/methylation_calling/{sample}-TechRep_{techrep}/{sample}-vector.rds"
-	conda:
-		"../envs/dmrcaller.yaml" if config["platform"] == 'linux' else ''
-	log:
-		outdir+"logs/methylation_calling/{sample}-{techrep}.log"
-	resources:
-		cpus=lambda wildcards : 4*config['params']['bismark']['instances'],
-		mem_mb= lambda  Input : int(genomeSize*11*4*len(Input)),
-		time_min=1440
-	script:
-		"../scripts/read_report.R"