Reference.md

@@ -65,13 +65,17 @@ graph TD;
   s3-->s4[assignment];
   s0--> id0b{{demultiplex.csv}};
 
-  id1[`run` paired-end .fastq files]-->r1(illuminapairedend);
+  id1[`run` paired-end .fastq files]-->opt1{illuminapairend:nb_chunk is greater than 0 ?};
 
   subgraph g1[assembly]
   
-  opt1{illuminapairend:nb_chunk == 0}
+  opt1 --> choice1a[YES]
+  opt1 --> choice1b[NO]
   
-  r1(illuminapairedend)-->r2(remove_unaligned);
+  choice1a --> r1a(split_fastq);
+  choice1b --> r1
+
+  r1-->r2(remove_unaligned);
   click r1 "https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/02_assembly/rules/illuminapairedend.smk";
   click r2 "https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/02_assembly/rules/remove_unaligned.smk";
   end