Fix doc for Trinity

Fix Trinity doc, attempt 2

content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/_index.md

@@ -5,7 +5,7 @@ weight = "52"
 +++
 
 
-[Trinity](https://github.com/trinityrnaseq/trinityrnaseq/wiki) is a method for efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: `Inchworm`, `Chrysalis`, and `Butterfly`. All these modules can be applied sequentially to process large RNA-Seq datasets.
+[Trinity](https://github.com/trinityrnaseq/trinityrnaseq/wiki) is a method for efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines four independent software modules: `Normalization`, `Inchworm`, `Chrysalis` and `Assembly`. All these modules can be applied sequentially to process large RNA-Seq datasets.
 
 
 The basic usage of Trinity is:
@@ -24,25 +24,25 @@ Running the Trinity pipeline from beginning to end on large datasets may exceed
 
 {{% panel theme="info" header="Step 1 Options" %}}
 {{< highlight bash >}}
-Trinity.pl [options] --no_run_chrysalis
+Trinity [options] --no_run_inchworm
 {{< /highlight >}}
 {{% /panel %}}
 
 {{% panel theme="info" header="Step 2 Options" %}}
 {{< highlight bash >}}
-Trinity.pl [options] --no_run_quantifygraph
+Trinity [options] --no_run_chrysalis
 {{< /highlight >}}
 {{% /panel %}}
 
 {{% panel theme="info" header="Step 3 Options" %}}
 {{< highlight bash >}}
-Trinity.pl [options] --no_run_butterfly
+Trinity [options] --no_distributed_trinity_exec
 {{< /highlight >}}
 {{% /panel %}}
 
 {{% panel theme="info" header="Step 4 Options" %}}
 {{< highlight bash >}}
-Trinity.pl [options]
+Trinity [options]
 {{< /highlight >}}
 {{% /panel %}}