add missing comma, and fix dev prints

bin/normalizedReadCount

@@ -244,24 +244,10 @@ if __name__ == "__main__":
     writeBam(inbam=BAM1, outbam=outbam1, commonReads=commonReads)
     writeBam(inbam=BAM2, outbam=outbam2, commonReads=commonReads)
 
-    print("nb1", nb1)
-    print("nb2", nb2)
-    print("gs1", gs1)
-    print("gs2", gs2)
-
     NormalizedReadRatio = log2((nb1 / gs1) / (nb2 / gs2))
 
     # Template output file structure
     # Sample_name,Organism_name1,Organism_name2,Genome1_size,Genome2_size,nb_bp_aligned_genome1,nb_bp_aligned_genome2,NormalizedReadRatio
-
-    print(SNAME)
-    print(ORGANAME1)
-    print(ORGANAME2)
-    print(gs1)
-    print(gs2)
-    print(nb1)
-    print(nb2)
-    print(NormalizedReadRatio)
     with open(OUTFILE, 'w') as w:
         w.write(SNAME + "," + ORGANAME1 + "," + ORGANAME2 + "," + str(gs1) + "," +
                 str(gs2) + "," + str(nb1) + "," + str(nb2) + "," + str(NormalizedReadRatio) + "\n")

bin/plotAndReport

@@ -74,7 +74,7 @@ def write_csv(adict, CSV):
         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")
+                    ["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__":

main.nf

@@ -214,7 +214,7 @@ process renameGenome1 {
     input:
         file (genome) from genome1rename
     output:
-        file ("*.fa") into (genome1Fasta, genome1Size, genome1Log, genome1mapdamage)
+        file (params.name1+".fa") into (genome1Fasta, genome1Size, genome1Log, genome1mapdamage)
     script:
         outname = params.name1+".fa"
         """
@@ -228,7 +228,7 @@ process renameGenome2 {
     input:
         file (genome) from genome2rename
     output:
-        file ("*.fa") into (genome2Fasta, genome2Size, genome2Log, genome2mapdamage)
+        file (params.name2+".fa") into (genome2Fasta, genome2Size, genome2Log, genome2mapdamage)
     script:
         outname = params.name2+".fa"
         """

nextflow.config

@@ -11,8 +11,6 @@ profiles {
             index2 = 'data/genomes/ecoli/Bowtie2Index/*.bt2'
             genome1 = 'data/genomes/bsubtilis/genome.fa'
             genome2 = 'data/genomes/ecoli/genome.fa'
-            genome1Size = 4215606
-            genome2Size = 4686137
             name1 = "Bacillus_subtilis"
             name2 = "Escherichia_coli"
             phred = 64