Fix doc for Trinity

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 %}}
 

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

@@ -7,7 +7,7 @@ weight = "10"
 
 ## Running Trinity with Paired-End fastq data with 8 CPUs and 100GB of RAM
 
-The first step of running Trinity is to run Trinity with the option **--no_run_chrysalis**:
+The first step of running Trinity is to run Trinity with the option **--no_run_inchworm**:
 {{% panel header="`trinity_step1.submit`"%}}
 {{< highlight bash >}}
 #!/bin/sh
@@ -21,12 +21,12 @@ The first step of running Trinity is to run Trinity with the option **--no_run_c
 
 module load trinity
 
-Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_chrysalis
+Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_inchworm
 {{< /highlight >}}
 {{% /panel %}}
 
 
-The second step of running Trinity is to run Trinity with the option **--no_run_quantifygraph**:
+The second step of running Trinity is to run Trinity with the option **--no_run_chrysalis**:
 {{% panel header="`trinity_step2.submit`"%}}
 {{< highlight bash >}}
 #!/bin/sh
@@ -40,12 +40,12 @@ The second step of running Trinity is to run Trinity with the option **--no_run_
 
 module load trinity
 
-Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_quantifygraph
+Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_chrysalis
 {{< /highlight >}}
 {{% /panel %}}
 
 
-The third step of running Trinity is to run Trinity with the option **--no_run_butterfly**:
+The third step of running Trinity is to run Trinity with the option **--no_distributed_trinity_exec**:
 {{% panel header="`trinity_step3.submit`"%}}
 {{< highlight bash >}}
 #!/bin/sh
@@ -59,7 +59,7 @@ The third step of running Trinity is to run Trinity with the option **--no_run_b
 
 module load trinity
 
-Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_butterfly
+Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_distributed_trinity_exec
 {{< /highlight >}}
 {{% /panel %}}
 
@@ -89,5 +89,5 @@ Trinity outputs number of files in its `trinity_out/` output directory after eac
 
 
 {{% notice tip %}}
-The Inchworm (step 1) and Chrysalis (step 2) steps can be memory intensive. A basic recommendation is to have **1GB of RAM per 1M ~76 base Illumina paired-end reads**.
+The Inchworm (step 2) and Chrysalis (step 3) steps can be memory intensive. A basic recommendation is to have **1GB of RAM per 1M ~76 base Illumina paired-end reads**.
 {{% /notice %}}