How to start

Required files

Samplesheet

The pipeline requires a samplesheet

# Create the column files
  ls FASTQ/RAW | awk -F'_R' '{ print $1 }'| sort | uniq > rawsample
  awk -F'_S[0-9]' '{ print $1 }' rawsample > sample_name
  awk -F'_L' '{ print "L"$2 }' rawsample > lane
# Paste the proper file endings to the rawsamples
  sed -e 's/$/_R1_001.fastq.gz/' rawsample > read1
  sed -e 's/$/_R2_001.fastq.gz/' rawsample > read2
# Combine the files
  paste -d'\t' rawsample sample_name lane read1 read2 > samplesheet.tsv
# Add the header line
  sed -i '1s/^/rawsample\tsample_name\tlane\tread1\tread2\n/' samplesheet.tsv
# Remove the temporary files
  rm rawsample sample_name lane read1 read2