Updating documentation and images

bio-raum · Sep 10, 2024 · ab7ea4e · ab7ea4e
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diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@
 
 If you are really impatient, check out our [quickstart](docs/quickstart.md) guide. 
 
-![schema](images/GABI_Schema_v4.png)
+![schema](images/GABI_Schema_v5.png)
 
 ## Documentation 
 

diff --git a/docs/output.md b/docs/output.md
@@ -49,6 +49,8 @@ QUAST provides some insights into the assembly quality - with some caveats conce
 
 ![quast](../images/multiqc_quast.png)
 
+Also see our [troubleshooting](troubleshooting.md) document for more explanations on the limitation of Quast as used by GABI. 
+
 #### Busco
 
 BUSCO identifies the presence of expected conserved bacterial genes - a good assembly should be near-complete and not contain (many) duplicated BUSCOs. 

diff --git a/images/GABI_Schema_v4.png b/images/GABI_Schema_v4.png
diff --git a/images/GABI_Schema_v5.png b/images/GABI_Schema_v5.png
diff --git a/images/multiqc_busco.png b/images/multiqc_busco.png
diff --git a/images/multiqc_confindr.png b/images/multiqc_confindr.png
diff --git a/images/multiqc_general_stats.png b/images/multiqc_general_stats.png
diff --git a/images/multiqc_kraken.png b/images/multiqc_kraken.png
diff --git a/images/multiqc_quast.png b/images/multiqc_quast.png
diff --git a/workflows/gabi.nf b/workflows/gabi.nf
@@ -372,7 +372,7 @@ workflow GABI {
         REPORT(
             ch_reports_grouped
         )
-        }
+    }
 
     /*
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-Original file line number
+Diff line change
@@ Expand Up / @@ -372,7 +372,7 @@ workflow GABI { @@
             REPORT(
                 ch_reports_grouped
             )
-            }
+        }
         /*
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ Expand Down @@