Tool:Shell script to automate trimmomatic for multiple samples

Question

[lakhujanivijay]

Couple of months back, I had developed this shell script to automate trimmomatic for multiple paired end fastq files. I could see multiple posts on biostars and I believe this is a routine work at many institutions.

Availability:

Hosted on GitHub

Feedback is highly appreciated

• Reach me on GitHub

  or

• Post comments here on Biostars

---

[Pierre Lindenbaum]

thanks for sharing. IMHO, you should have a look at solutions like nextflow or snakemake.

[lakhujanivijay]

Hi Pierre Lindenbaum

I completely agree with you on that. I should start learning. Thanks for the suggestion.

[cpad0112]

Thanks for sharing the params.

[lakhujanivijay]

Thanks cpad0112

Answer 1

[ATpoint]

Suggestion for improvement: Check up front at the beginning of a script that all necessary tools are in PATH and/or defined in variables, e.g.:

## $TRIMMOMATIC could be a path like $HOME/software/trimmomatic.jar
TOOLS=(samtools bedtools bowtie2 $TRIMMOMATIC)

## A simple command that checks if tools can be found, if not names are written to a file <missing_tools.txt>
function PathCheck {

  if [[ $(command -v $1 | wc -l) == 0 ]]; then 
    echo ${1} >> missing_tools.txt
    fi

}; export -f PathCheck

## Check all tools:
for i in $(echo ${TOOLS[*]}); do
  PathCheck $i; done

## If any of the specified tools is missing, throw an error and exit:
if [[ -e missing_tools.txt ]] && [[ $(cat missing_tools.txt | wc -l | xargs) > 0 ]]; then
  echo '[ERROR] Missing tools -- see missing_tools.txt for details' && exit 1
  fi

[lakhujanivijay]

Thanks for the awesome suggestion ATpoint. That's worth implementing!