Demultiplexing and convert fastq into tsv

#!/bin/bash

#
# Script Name: preprocessing.sh
# Description:
#   - Demultiplex metabarcoding paired end fastq files using cutadapt
#   - Transform fastq files into tab files using seqkit
#   - Join R1 and R2 tab files
# Requirements: cutadapt, seqkit, gnumeric
# Arguments:
#   - corr_tag_file: an excel file provided by SPYGEN describing the correspondences between tags and samples
#   - fastq_dir: Folder directory containing fastq files
# Author: Morgane Bruno
# Email: morgane.bruno@cefe.cnrs.fr
# Licence: MIT
# Usage: bash preprocessing.sh corr_tag.xlsx path/to/fastq/
#

#_input
corr_tag_file=$1
fastq_dir=$2
out_path="01_demultiplex/"

#_main
mkdir -p $out_path

# GNUMERIC: Convert XLSX into CSV
metadata_path="${out_path}corr_tag/"
mkdir -p $metadata_path
xlsx_base=$(basename $corr_tag_file .xlsx)
corr_tag_csv="${metadata_path}${xlsx_base}.csv"
if [ ! -f "$corr_tag_csv" ]; then
  ssconvert $corr_tag_file $corr_tag_csv 
fi

# Check corr_tag column name
run_idx=$(head -n 1 $corr_tag_csv | tr "," "\n" | grep -n "^RUN$")
if [ -z "${run_idx}" ]; then 
  echo "::error:: Missing column: RUN"
  exit 0
fi
tag_idx=$(head -n 1 $corr_tag_csv | tr "," "\n" | grep -n "^TAG$")
if [ -z "${tag_idx}" ]; then 
  echo "::error:: Missing column: TAG"
  exit 0
fi
sample_idx=$(head -n 1 $corr_tag_csv | tr "," "\n" | grep -n "^SAMPLE$")
if [ -z "${sample_idx}" ]; then
  echo "::error:: Missing column: SAMPLE"
  exit 0
fi

# Extract RUN name
run_name=$(awk -F"," -v idx=$run_idx 'NR>1 {h[$idx]++} END{for(run in h) print run}' $corr_tag_csv)

# Demultiplexing
for run in $run_name
do
  echo "::info:: Start demultiplexing ${run} ..."
  run_outdir="${out_path}${run}/"
  mkdir -p $run_outdir
  awk -F',' -v r=$run -v ridx=$run_idx -v sidx=$sample_idx -v tidx=$tag_idx -v path=$run_outdir '($ridx == r) {
  if ($sidx ~ /SPY/) {
    split($tidx, tag5, "");
    tag3 = "";
    for (i = length(tag5); i > 0; i--) {
      nt = tag5[i];
      if (nt ~ /c/) tag3 = tag3 "g";
      if (nt ~ /g/) tag3 = tag3 "c";
      if (nt ~ /t/) tag3 = tag3 "a";
      if (nt ~ /a/) tag3 = tag3 "t";
    }
    print ">" path "/" $sidx "\n" $tidx "..." tag3
   }
  } ' $corr_tag_csv > $run_outdir/tags_cutadapt.fa
  if [ -s $run_outdir/tags_cutadapt.fa ]; then # if SPY filter in RUN
    # Check fastq files
    fq_r1=$(find $fastq_dir -name *$run*R1*)
    if [ -z "${fq_r1}" ]; then
      echo "::error:: Missing file for run: ${run}"
      exit 0
    fi
    fq_r2=$(echo $fq_r1 | sed 's/R1/R2/')
    # CUTADAPT: DEMULTIPLEXING
    cutadapt --revcomp -O 8 --no-indels  -g file:$run_outdir/tags_cutadapt.fa -G file:$run_outdir/tags_cutadapt.fa --output {name}.1.fastq.gz --paired-output {name}.2.fastq.gz $fq_r1 $fq_r2
    # SEQKIT: Convert FASTQ  into TSV
    for sample_r1 in $run_outdir*1.fastq.gz
    do
      tab_r1=$(echo $sample_r1 | sed 's/gz/tsv/')
      csv_r1=$(echo $sample_r1 | sed 's/gz/csv/')
      seqkit fx2tab -Q $sample_r1 > $tab_r1
      awk -F' ' '{ print $1 "," $3 }' $tab_r1 > $csv_r1
      sample_r2=$(echo $sample_r1 | sed 's/1.fastq/2.fastq/')
      tab_r2=$(echo $sample_r2 | sed 's/gz/tsv/')
      csv_r2=$(echo $sample_r2 | sed 's/gz/csv/')
      seqkit fx2tab -Q $sample_r2 > $tab_r2
      awk -F' ' '{ print $1 "," $3 }' $tab_r2 > $csv_r2
      csv_out=$(echo $sample_r1 | sed 's/1.fastq.gz/csv/')
      echo "Forward,Reverse" > $csv_out
      join -t$',' -o1.2,2.2 -e "NA" $csv_r1 $csv_r2 >> $csv_out
      rm $tab_r1
      rm $tab_r2
      rm $csv_r1
      rm $csv_r2
    done
  else
    echo "::info:: No SPY filters were processed in run: ${run}"
    rm -r $run_outdir
  fi
done