Add scratch to Trinity example

Add scratch to Trinity example

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

@@ -14,6 +14,10 @@ $ Trinity --seqType [fa|fq] --max_memory <maximum_memory> --left input_reads_pai
 {{< /highlight >}}
 where **input_reads_pair_1.[fa|fq]** and **input_reads_pair_2.[fa|fq]** are the input paired-end files of sequence reads in fasta/fastq format, and **--seqType** is the type of these input reads. The option **--max_memory** specifies the maximum memory to use with Trinity.
 
+{{% notice info %}}
+**Trinity produces many intermediate files that can affect the file system. To avoid any issues, please copy all the input data to the faster local storage called "scratch", store the output in "scratch" and finally copy all the needed output files from "scratch" to /work. The "scratch" directories are unique per job and are deleted when the job finishes. This can greatly improve performance!**
+{{% /notice %}}
+
 Additional Trinity **options** can be found in the Trinity website, or by typing:
 {{< highlight bash >}}
 $ Trinity