Shell Programming and Scripting

for f in $(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta") # -v -> exclude
do
  sed -i 's/%[^:]*//' "$f"
done

custom=$(echo "${customFields[@]}" | sed -e 's/ /\\t/g') #add custom
echo -e "#SampleID\tBarcodeSequence\tLinkerPrimerSequence\tInputFileName\t"${custom}"\tDescription" > "${metadata}"/metadata.tsv

for g in $(find "$trimmed" -type f | grep "fasta" | grep -v "scrap") # -v -> exclude
do
  name=$(basename "$g")
  nameNoExt="${name%.*}"
  #create array: a=(1 2 3 4)
  #show content of array: echo "${a[@]}"
  #t="${nameNoExt//-/ }"
  #params=("${nameNoExt//-/ }") #${string//substring/replacement}
  #echo "${params[@]}"
  param1=$(cut <<< "$nameNoExt" -d "-" -f 1) #equals $(echo "$nameNoExt" | cut -d "-" -f 1)
  param2=$(cut <<< "$nameNoExt" -d "-" -f 2)
  param3=$(cut <<< "$nameNoExt" -d "-" -f 3 | sed -e 's/Run//') #only keep the number of the run

  tempLine=$(cat "$barcode" | grep "$param1" | grep "$param2" | grep "$param3")
  echo "$tempLine" | awk -v fileName="$name" -v sampleName="$its" -F $'\t' 'BEGIN {OFS = FS} {print $1, $3, $4, fileName, $6, $7, $8, $9, $10, $1"-"sampleName}' >> "${metadata}/metadata.tsv"
done