Trimmomatic loop

#trimmomatic loop, from: https://github.com/raynamharris/Shell_Intro_for_Bioinformatics_STG/blob/master/lessons/06_ForLoops.md

for R1 in *R1*
do
   R2=${R1//R1_001.fastq/R2_001.fastq}
  R1paired=${R1//.fastq/_paired.fastq}
  R1unpaired=${R1//.fastq/_unpaired.fastq}
  R2paired=${R2//.fastq/_paired.fastq}
  R2unpaired=${R2//.fastq/_unpaired.fastq}
  echo "java -jar trimmomatic-0.39.jar PE -phred33 $R1 $R2 $R1paired $R1unpaired $R2paired $R2unpaired ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 -threads 32"  >> trimmomatic.cmds
done

# Then run trimmomatic.cmds
cat trimmomatic.cmds