Description of organelles subworkflow

docs/output.md

@@ -146,8 +146,23 @@ This subworkflow is used to evaluate the quality of sequences. It is performed a
 ![Genome statistics subworkflow](https://raw.githubusercontent.com/sanger-tol/genomeassembly/documentation/docs/images/v1/genome_statistics.png)
 
 ### ORGANELLES
-Implements steps to assemble the mitogenome</p> 
 
+<details markdown="1">
+  <summary>Output files</summary>
+
+  - <code>final_mitogenome.fasta</code>
+    - organelle assembly
+  - <code>final_mitogenome.[gb,gff]</code>
+    - organelle gene annotation
+  - <code>contigs_stats.tsv</code>
+    - summary of mitochondrial findings
+  - output also includes other output files produced by MitoHiFi
+
+</details>
+
+This subworkflow implements assembly of organelles. In the main pipeline it is called twice - for assembling mitochondrion from HiFi reads and as an alternative it runs identification of the mitochondrion for the genome assembly </p> 
+
+![Organelles subworkflow](https://raw.githubusercontent.com/sanger-tol/genomeassembly/documentation/docs/images/v1/organelles.png)
 
 ### Pipeline information