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bqsr_merge_make_input.sh
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bqsr_merge_make_input.sh
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#!/bin/bash
##########################################################################
#
# Platform: NCI Gadi HPC
# Usage: bash bqsr_merge_make_input.sh <config prefix>
# Version: 2.0
#
# For more details see: https://github.com/Sydney-Informatics-Hub/Fastq-to-BAM
#
# If you use this script towards a publication, please acknowledge the
# Sydney Informatics Hub (or co-authorship, where appropriate).
#
# Suggested acknowledgement:
# The authors acknowledge the support provided by the Sydney Informatics Hub,
# a Core Research Facility of the University of Sydney. This research/project
# was undertaken with the assistance of resources and services from the National
# Computational Infrastructure (NCI), which is supported by the Australian
# Government, and the Australian BioCommons which is enabled by NCRIS via
# Bioplatforms Australia funding.
#
##########################################################################
cohort=../$1
dict=
contigs=$(awk '$2~/^SN/ {print $2}' $dict | sed 's/SN\://')
contigs=($contigs)
contigs+=( "unmapped" )
num_recal=$((${#contigs[@]}-1)) # Count starts at 0
group=false
t_input=./Inputs/bqsr_merge.inputs-tumour
n_input=./Inputs/bqsr_merge.inputs-normal
input=./Inputs/bqsr_merge.inputs
rm -f $t_input
rm -f $n_input
rm -f $input
# Make BQSR merge list
# List of bam files to merge per sample
mkdir -p ./Inputs/BQSR_merge_lists
while read -r sampleid labid seq_center library; do
if [[ ! ${sampleid} =~ ^#.*$ ]]; then
list=./Inputs/BQSR_merge_lists/${labid}.list
\rm -rf $list
for i in $(seq 0 ${num_recal})
do
printf "../BQSR_apply/${labid}.${i}.recal.bam\n" >> $list
done
fi
done < "${cohort}.config"
# Make input list
while read -r sampleid labid seq_center library; do
if [[ ! ${sampleid} =~ ^#.*$ ]]
then
if [[ $group = true ]]
then
if [[ ${labid} =~ -B$ || ${labid} =~ -N$ ]]
then
printf "${labid}\n" >> $n_input
else
printf "${labid}\n" >> $t_input
fi
else
printf "${labid}\n" >> $input
fi
fi
done < "${cohort}.config"
if [ -f $input ]
then
tasks=`wc -l < $input`
printf "Number of BQSR merge tasks to run: ${tasks}\n"
fi
if [ -f $n_input ]
then
tasks=`wc -l < $n_input`
printf "Number of BQSR merge normal sample tasks to run: ${tasks}\n"
fi
if [ -f $t_input ]
then
tasks=`wc -l < $t_input`
printf "Number of BQSR merge tumour sample tasks to run: ${tasks}\n"
fi