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ENA_manifest_files.sh
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ENA_manifest_files.sh
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#!/bin/bash
#
# Script to create the manifest file for multiple individuals
# Author: Luis J. Chueca
#
# Modify reads information accordingly to your data
# FILE.txt has to be a two column file with sample alias in column 1 and ENA accession number in column 2
#
# usage: ./ENA_manifest_files.sh FILE.txt STUDY_NUMBER
# e.g.: ./ENA_manifest_files.sh sample_name_ids.txt PRJEB43841
#
while read i b; do
echo "i is $i, b is $b"
# Provide necessary information on how reads were obtained (see https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html)
#INSTRUMENT
INS="Illumina NovaSeq 6000"
#INSERT_SIZE
ISZ="300"
#LIBRARY_SOURCE
LSC="GENOMIC"
#LIBRARY_SELECTION
LST="RANDOM"
#LIBRARY_STRATEGY
LSG="WGS"
echo "STUDY $2" > "${i}_manifest.txt"
echo "SAMPLE ${b}" >> "${i}_manifest.txt"
echo "NAME ${i}" >> "${i}_manifest.txt"
echo "INSTRUMENT ${INS}" >> "${i}_manifest.txt"
echo "INSERT_SIZE ${ISZ}" >> "${i}_manifest.txt"
echo "LIBRARY_SOURCE ${LSC}" >> "${i}_manifest.txt"
echo "LIBRARY_SELECTION ${LST}" >> "${i}_manifest.txt"
echo "LIBRARY_STRATEGY ${LSG}" >> "${i}_manifest.txt"
# Go into directory and loop over files ending with fq.gz
cd "$i"
for file in *fq.gz; do
echo "FASTQ $(basename "$file")" >> "../${i}_manifest.txt"
done
cd ..
# Move the generated manifest file to the respective directory
mv "${i}_manifest.txt" "${i}/"
done < $1 > "$2"_stdout.log 2> "$2"_stderr.log