Reference.md

@@ -53,8 +53,6 @@ graph TD;
   classDef Configurer fill:#E0FFFF;
   classDef Snakefile fill:#98FB98,border:#0c4c0c;
  
-
- 
   id0s{{`marker` sample description .dat}}-->s0;
   id0c{{config.yaml}}-->s0;
  id0a{{rapdirun.tsv}}-->s0;
@@ -63,10 +61,8 @@ graph TD;
   s1-->s2[demultiplexing];
   s2-->s3[filtering];
   s3-->s4[assignment];
-
   s0--> id0b{{demultiplex.csv}};
 
-
   id1[`run` paired-end .fastq files]-->r1(illuminapairedend);
 
   subgraph g1[assembly]
@@ -116,16 +112,14 @@ graph TD;
   click r13 "https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/05_assignment/rules/table_runs.smk";  
   end
 
-  r13-->id6[`projet`/`marker`/`run` species occurence .tsv files];
+  bdr(`marker` reference database)-->r10
 
+  r13-->id6[`projet`/`marker`/`run` species occurence .tsv files];
 
 
     
   id0a-->s1;
-
-
-
-  id0b-->s2;
+  id0a-->s2;
   id0b-->s3;
   id0b-->s4;
 
@@ -220,7 +214,7 @@ Run : R2 .fastq.gz file path
 
 The [assembly Snakefile](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/02_assembly/Snakefile) will use the wildcards `run` deduced from [rapidrun.tsv](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/resources/test/all_samples.tsv) and performs the following rules:
 
-#### Align and merge paired-end reads
+#### 2.1 Align and merge paired-end reads
 
 [illuminapairedend](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/02_assembly/rules/illuminapairedend.smk): paired end alignment then keep reads with quality > s_min
 * inputs:
@@ -231,7 +225,7 @@ The [assembly Snakefile](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidr
 * output:
   * results/02_assembly/01_illuminapairedend/`run`.fastq: merged sequences fastq file
 
-#### Remove unaligned sequence records
+#### 2.2 Remove unaligned sequence records
 
 [remove_unaligned](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/02_assembly/rules/remove_unaligned.smk): merged sequence tagged as "unaligned" are removed
 
@@ -241,7 +235,9 @@ The [assembly Snakefile](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidr
   * results/02_assembly/02_remove_unaligned/`run`.ali.fastq: aligned and merged sequences fastq file
 
 
-### 3 Demultiplexing
+#### 3. Demultiplexing
+
+
 
 
 ### 4 Filtering