Fix missing script.

workflow/main.nf

@@ -13,6 +13,7 @@ params.bwaIndex = params.genome ? params.genomes[ params.genome ].bwa ?: false :
 params.genomeSize = params.genome ? params.genomes[ params.genome ].genomesize ?: false : false
 params.chromSizes = params.genome ? params.genomes[ params.genome ].chromsizes ?: false : false
 params.tssFile = params.genome ? params.genomes[ params.genome ].tssfile ?: false : false
+params.cutoffRatio = 1.2
 
 // Check inputs
 if( params.bwaIndex ){

workflow/scripts/atac_qc.py

@@ -38,7 +38,15 @@ def get_args():
                         required=True)
 
     parser.add_argument('-p', '--prefix',
-                        help="The Predix of the file.",
+                        help="The Prefix of the file.",
+                        required=True)
+
+    parser.add_argument('-t', '--tss',
+                        help="The TSS file to use as QC.",
+                        required=True)
+
+    parser.add_argument('-c', '--chromsizes',
+                        help="The chromsizes file to use as QC.",
                         required=True)
 
     args = parser.parse_args()
@@ -49,10 +57,14 @@ def main():
     args = get_args()
     prefix = args.prefix
     bam = args.bam
+    tss = args.tss
+    chromsizes = args.chromsizes
 
     bins=400
+    bp_edge = 2000
 
-    tss_ext = pybedtools.BedTool('../data/hg19_gencode_tss_unique_2kb.bed')
+    tss = pybedtools.BedTool(tss)
+    tss_ext = tss.slop(b=bp_edge, g=chromsizes)
 
     bam = metaseq.genomic_signal(bam, 'bam') # Need to shift reads and just get ends, just load bed file?
     bam_array = bam.array(tss_ext, bins=bins, shift_width = -75/2, stranded=True, processes=cpu_count())