output csv table

bin/plotAndReport

@@ -30,6 +30,12 @@ def get_args():
         default=None,
         help='coproID version'
     )
+    parser.add_argument(
+        "-csv",
+        dest="csv",
+        default=None,
+        help="csv filename output. Default = coproid.csv"
+    )
     parser.add_argument(
         '-o',
         dest="output",
@@ -42,8 +48,9 @@ def get_args():
     identity = float(str(args.identity))
     version = str(args.version)
     outfile = args.output
+    csv = args.csv
 
-    return(countFile, identity, version, outfile)
+    return(countFile, identity, version, outfile, csv)
 
 
 def getBasename(file_name):
@@ -62,8 +69,16 @@ def getFile(path):
     return(filename)
 
 
+def write_csv(adict, CSV):
+    with open(CSV, "w") as f:
+        f.write("Sample_name,Organism_name1,Organism_name2,Genome1_size,Genome2_size,nb_aDNA_bp_aligned_genome1,nb_aDNA_bp_aligned_genome2,NormalizedReadRatio\n")
+        for akey in adict:
+            f.write(akey + "," + adict[akey]["orga1"] + "," + adict[akey]
+                    ["orga2"] + "," + str(adict[akey]["gs1"]) + "," + str(adict[akey]["gs2"]) + str(adict[akey]["nbp1"]) + "," + str(adict[akey]["nbp2"]) + "," + str(adict[akey]["nrr"]) + "\n")
+
+
 if __name__ == "__main__":
-    CF, ID, VERSION, OUTFILE = get_args()
+    CF, ID, VERSION, OUTFILE, CSV = get_args()
 
     identity = ID * 100
 
@@ -98,6 +113,8 @@ if __name__ == "__main__":
             d[sample]["nbp2"] = nbp2
             d[sample]["nrr"] = nrr
 
+    write_csv(d, CSV)
+
     orga1_clean = organism1.replace("_", " ")
     orga2_clean = organism2.replace("_", " ")
 

main.nf

@@ -581,15 +581,19 @@ process proportionAndReport {
 
     label 'ristretto'
 
+    publishDir "${params.results}", mode: 'copy', pattern: '*.csv'
+
     input:
         file(count) from coproid_count
     output:
         file("*.md") into coproidmd
         file("*.png") into plot
+        file("*.csv") into csv_out
     script:
         outfile = "coproID_result.md"
+        csvout = "coproid_result.csv"
         """
-        plotAndReport -c $count -i ${params.identity} -v $version -o $outfile
+        plotAndReport -c $count -i ${params.identity} -v $version -csv $csvout -o $outfile
         """
 }