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SBATCH trinity for multiple files and rename/move the output files

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# 1  
Old 08-23-2016
Code SBATCH trinity for multiple files and rename/move the output files
Hey guys,
I have wrote the following script to apply a module named "trinity" on my files. (it takes two input files and spit a trinity.fasta as output)
Code:
#!/bin/bash -l
#SBATCH -p node
#SBATCH -A <projectID>
#SBATCH -n 16
#SBATCH -t 7-00:00:00
#SBATCH --mem=128GB 
#SBATCH --mail-type=ALL
#SBATCH --mail-user=<email address>
#SBATCH -o /path/to/log/file
#SBATCH -e /path/to/error/file
#SBATCH -J trinity

module load bioinfo-tools trinity

Trinity --seqType fq --max_memory 120G --CPU 16 \
--left /path/to/first/input/input1.fq \
--right /path/to/second/input/input2.fq \
--normalize_reads --SS_lib_type RF --no_bowtie --output /path/to/output/directory/trinity_out_dir

Now I cannot figure out how to modify this to take multiple files (2 inputs in each iteration) and then rename the output file (which is "trinity.fasta") and move it to another folder so it won't be overwritten every time.
all my files are like this:
Code:
Sample1_1.fq
Sample1_2.fq

sample2_1.fq
Sample2_2.fq
...

and obviously the desired outputs:
Code:
Sample1.fasta, Sample2.fasta, ...

Thanks in advance!
# 2  
Old 08-23-2016
Code:
for ((N=1; N<=20; N++))
do
        something file${FILE}_1 file${FILE}_2
        mv output_file somewhere
done

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