jupyter for concatenate detection

cnvpipelines.py

@@ -19,7 +19,7 @@ from subprocess import run
 
 TOOLS = ["lumpy", "delly", "pindel", "genomestrip"]
 VTYPES = ["DEL", "INV", "DUP", "mCNV"]
-MIN_CHR_SIZE = 50000
+MIN_CHR_SIZE = 500000
 
 MD5_TEST = {
     "ERR470101_f_1.fq.gz": "2c30600e303c9bfb7b9538ec76055203",

snakecnv/common.smk

@@ -513,9 +513,9 @@ class MergeBatches(Detection):
                           chrom=self.chromosomes,
                           svtype=[x for x in self.varianttypes if x != "mCNV"])
         concat = expand("results/{svtype}/concat_{svtype}_final.vcf.gz", svtype=[x for x in self.varianttypes if x != "mCNV"])
-        #jupyter = ["results/detection_summary.html"]
+        jupyter = ["results/detection_summary.html"]
         
-        return outputs + concat # + jupyter
+        return outputs + concat + jupyter
     
     
         return outputs