Nanoplot.sh

#!/bin/bash

### do Nanoplot analysis

input=$1
output=$2
name=$3
barcoded=$4

mkdir $output

echo """
    #!/bin/sh

    ## name of Job
    #PBS -N ${name}

    ## Redirect output stream to this file.
    #PBS -o ${output}/log.txt

    ## Stream Standard Output AND Standard Error to outputfile (see above)
    #PBS -j oe

    ## Select a maximum of 200 cores and 200gb of RAM
    #PBS -l select=1:ncpus=50:mem=200gb

    ######## load dependencies #######

    source /opt/anaconda3/etc/profile.d/conda.sh
    conda activate nanoplot_1.39.0

    if [[ ${input} == *sequencing_summary.txt* ]]; then

      if [[ $barcoded == \"yes\" ]];then

        ######## run analyses #######
        NanoPlot \
          -t 50 \
          --summary ${input} \
          --maxlength 500000 \
          --barcoded \
          --plots dot -o ${output}/

        else

          ######## run analyses #######
          NanoPlot \
            -t 50 \
            --summary ${input} \
            --maxlength 500000 \
            --plots dot -o ${output}/
        fi

    else

    if [[ $barcoded == \"yes\" ]]
    then

      ######## run analyses #######
      NanoPlot \
        -t 50 \
        --fastq ${input} \
        --maxlength 500000 \
        --barcoded \
        --plots dot -o ${output}/

      else

        ######## run analyses #######
        NanoPlot \
          -t 50 \
          --fastq ${input} \
          --maxlength 500000 \
          --plots dot -o ${output}/
      fi
    fi



    ################ make pdf report_test_Damen #############
    pandoc -f html \
      -t markdown \
      -o ${output}/NanoPlot-report.md \
      ${output}/NanoPlot-report.html

    awk '1;/### Plots/{exit}' ${output}/NanoPlot-report.md \
    > ${output}/NanoPlot-report_cut.md

    for i in ${output}/*.png
    do
      File=\${i##*/}
      Name=\${File%.*}
      echo '!['\$Name']('\$i')' >> ${output}/NanoPlot-report_cut.md
    done

    pandoc -f markdown \
      -t latex \
      -o ${output}/NanoPlot-report_${name}.pdf \
      ${output}/NanoPlot-report_cut.md

    rm -f ${output}/NanoPlot-report*.md
    ######################
""" >${output}/qsub_nanoplot.sh

qsub ${output}/qsub_nanoplot.sh