better countBP output file name

nf-core · Oct 8, 2018 · ed580e6 · ed580e6
1 parent f1b1ad5
commit ed580e6
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Showing 2 changed files with 28 additions and 5 deletions.
diff --git a/bin/normalizedReadCount b/bin/normalizedReadCount
@@ -73,6 +73,18 @@ def get_args():
         default=None,
         help="Output file basename. Default = {BAM_GENOME}.out"
     )
+    parser.add_argument(
+        '-ob1',
+        dest="output_bam1",
+        default=None,
+        help="Output bam 1 filename. Default = {BAM1_INPUT}.filtered.bam"
+    )
+    parser.add_argument(
+        '-ob2',
+        dest="output_bam2",
+        default=None,
+        help="Output bam 2 filename. Default = {BAM2_INPUT}.filtered.bam"
+    )
     parser.add_argument(
         '-p',
         dest="processes",
@@ -93,9 +105,11 @@ def get_args():
     sname = args.name
     identity = float(str(args.identity))
     outfile = args.output
+    obam1 = args.output_bam1
+    obam2 = args.output_bam2
     processes = int(args.processes)
 
-    return(bam1, genome1, size1, organame1, bam2, genome2, size2, organame2, sname, identity, processes, outfile)
+    return(bam1, genome1, size1, organame1, bam2, genome2, size2, organame2, sname, identity, processes, outfile, obam1, obam2)
 
 
 def getBasename(file_name):
@@ -195,7 +209,7 @@ def getCommonReads(readsBam1, readsBam2):
 
 if __name__ == "__main__":
     # bam1, genome1, size1, organame1, outfile1, bam2, genome2, size2, organame2, outfile2, sname, identity, processes
-    BAM1, GENOME1, SIZE1, ORGANAME1, BAM2, GENOME2, SIZE2, ORGANAME2, SNAME, ID, PROCESSES, OUTFILE = get_args()
+    BAM1, GENOME1, SIZE1, ORGANAME1, BAM2, GENOME2, SIZE2, ORGANAME2, SNAME, ID, PROCESSES, OUTFILE, OBAM1, OBAM2 = get_args()
 
     if BAM1 is None:
         print("Missing BAM file")
@@ -236,8 +250,15 @@ if __name__ == "__main__":
     nb2 = getNumberMappedReadsMultiprocess(
         bam=BAM2, processes=PROCESSES, id=ID, commonReads=commonReads)["bpCnt"]
 
-    outbam1 = bam_basename1 + ".filtered.bam"
-    outbam2 = bam_basename2 + ".filtered.bam"
+    if OBAM1 is None:
+        outbam1 = bam_basename1 + ".filtered.bam"
+    else:
+        outbam1 = OBAM1
+    if OBAM2 is None:
+        outbam2 = bam_basename2 + ".filtered.bam"
+    else:
+        outbam2 = OBAM2
+
     writeBam(inbam=BAM1, outbam=outbam1, commonReads=commonReads)
     writeBam(inbam=BAM2, outbam=outbam2, commonReads=commonReads)
 

diff --git a/main.nf b/main.nf
@@ -490,10 +490,12 @@ process countBp{
         outfile = name+".out"
         organame1 = params.name1
         organame2 = params.name2
+        obam1 = name+"_"+organame1+".filtered.bam"
+        obam2 = name+"_"+organame2+".filtered.bam"
         """
         samtools index $bam1
         samtools index $bam2
-        normalizedReadCount -n $name -b1 $bam1 -b2 $bam2 -g1 $genome1 -g2 $genome2 -r1 $organame1 -r2 $organame2 -i ${params.identity} -o $outfile -p ${task.cpus}
+        normalizedReadCount -n $name -b1 $bam1 -b2 $bam2 -g1 $genome1 -g2 $genome2 -r1 $organame1 -r2 $organame2 -i ${params.identity} -o $outfile -ob1 $obam1 -ob2 $obam2 -p ${task.cpus}
         """
 }