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skims_processing_pipeline.sh
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#!/bin/bash
set -e
set -x
out_dir=`pwd`
ref_dir=`pwd`
threads=8
iterations=1000
cores=8
interleaven_counter=0
usage="bash ${BASH_SOURCE[0]} -h [-x input] [-l interleaven_counter] [-g lib_dir] [-r threads] [-d iterations] [-f cores]
Runs nuclear read processing pipeline on a batch of reads split into two mates in reference to a constructed library:
Options:
-h show this help text
Mandatory inputs:
-x path to folder containing reads (split reads that need to be merged)
Optional inputs:
-l can be set as 0(default) or 1, input 1 if the input directory consists of single interleaved paired-end reads instead of two mate pair reads
-g path to reference library
-r threads for RESPECT; default: 8
-d number of iteration cycles for RESPECT, default: 1000
-f number of cores for SKMER, default: 8"
while getopts ":hl:x:r::d::f::g::" opts
do
case "$opts" in
h) echo "$usage"; exit;;
l) interleaven_counter="$OPTARG";;
x) input="$OPTARG";;
r) threads="$OPTARG";;
d) iterations="$OPTARG";;
f) cores="$OPTARG";;
g) lib_dir="$OPTARG";;
[?]) echo "invalid input param"; exit 1;;
esac
done
if [ ! "$input" ]; then
echo "arguments -x must be provided"; exit 1
fi
x=`ls $input`
if [ !$x ]; then
echo "No files in directory"
exit
fi
if [ "${input:0-1}" = "/" ]; then
input=${input%?}
fi
SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
if [ ! "$lib_dir" ]; then
if [ ! -d "$ref_dir/library" ]; then
mkdir $ref_dir/library
fi
lib_dir=$ref_dir/library
fi
if [ ! -f "$SCRIPT_DIR/log_file.txt" ]; then
echo "Log File for tracking operations">>$SCRIPT_DIR/log_file.txt
fi
if [ ! -f "$lib_dir/CONFIG" ]; then
echo "kmer_length 31
sketch_size 100000
sketching_seed 42" >$lib_dir/CONFIG
fi
if [ "1" -eq "$interleaven_counter" ]; then
echo "Entered first interleaven block"
bash ${SCRIPT_DIR}/interleaven.sh ${input} ${ref_dir}
input=${ref_dir}/interleaven_reads
fi
declare -A array
counter=0
for f in `ls ${input}`; do
genome=$(basename -- "$f")
extension="${genome##*.}"
if [ "$extension" = "gz" ]; then
genome="${genome%.*}"
extension="${genome##*.}"
if [ "$extension" = "fastq" ] || [ "$extension" = "fq" ] || [ "$extension" = "fna" ] || [ "$extension" = "fa" ]; then
genome="${genome%.*}"
if [ "$extension" = "fastq" ] || [ "$extension" = "fq" ]; then
genome="${genome%?}"
fi
key=$genome
counter=1
fi
elif [ "$extension" = "fastq" ] || [ "$extension" = "fq" ] || [ "$extension" = "fna" ] || [ "$extension" = "fa" ]; then
genome="${genome%.*}"
if [ "$extension" = "fastq" ] || [ "$extension" = "fq" ]; then
genome="${genome%?}"
fi
key=$genome
counter=1
fi
if [ "1" -eq "$counter" ]; then
value=$f
array[${key}]="${array[${key}]}${array[${key}]:+,}${value}"
counter=0
fi
done
direc_name=$(basename "${BASH_SOURCE[0]%.*}")
mkdir -p ${out_dir}/${direc_name}/{bbmap,assemblies,consult,kraken,respect}
if [ -d "${out_dir}/temp_ops" ]; then
echo "Temp folder found; removed for later operations"
rm -r ${out_dir}/temp_ops
fi
source ${SCRIPT_DIR}/conda_source.sh
for key in "${!array[@]}"; do
assembly_counter=0
genome=$key
genome_value=${array[$key]}
input_1="${genome_value%,*}"
extension_1="${input_1##*.}"
if [ "$extension_1" = "gz" ]; then
temp="${input_1%.*}"
extension_2="${temp##*.}"
if [ "$extension_2" = "fna" ] || [ "$extension_2" = "fa" ]; then
assembly_counter=1
zcat $input/$input_1 | cat > ${out_dir}/${direc_name}/assemblies/${genome}.fna
fi
elif [ "$extension_1" = "fna" ] || [ "$extension_1" = "fa" ]; then
assembly_counter=1
fi
if [ "0" -eq "$assembly_counter" ]; then
input_2="${genome_value#*,}"
fi
mkdir -p ${out_dir}/temp_ops
cd ${out_dir}/temp_ops
counter=0
if [ -f "${out_dir}/${direc_name}/bbmap/${genome}_merged.fq" ] && [ "0" -eq "$assembly_counter" ]; then
test_var=0
test_var=`grep "$genome" $SCRIPT_DIR/log_file.txt | grep -c -e "A$" -e "AD$" -e "ADE$" -e "ADEB$" -e "ADEBC$"` || true
if [ "1" -eq "$test_var" ]; then
counter=1
else
rm ${out_dir}/${direc_name}/bbmap/${genome}_merged.fq
fi
fi
extension="${input_1##*.}"
if [ "0" -eq "$counter" ] && [ "0" -eq "$assembly_counter" ]; then
echo "BBMap cleanup pipeline starts"
if [ "$extension" = "gz" ]; then
${SCRIPT_DIR}/bbmap_pipeline.sh ${input}/${input_1} ${input}/${input_2} ${out_dir}/${direc_name}/bbmap/${genome}_merged.fq
echo "BBMap cleanup pipeline ends"
else
${SCRIPT_DIR}/interleaved_bbmap_pipeline.sh ${input}/${input_1} ${input}/${input_2} ${out_dir}/${direc_name}/bbmap/${genome}_merged.fq
echo "BBMap cleanup pipeline ends"
fi
if [ -z "`grep "$genome" $SCRIPT_DIR/log_file.txt`" ]; then
echo "$genome""A">>$SCRIPT_DIR/log_file.txt
else
var=`grep "$genome" $SCRIPT_DIR/log_file.txt`
var1="$genome""IA"
sed -i "s/$var/$var1/" $SCRIPT_DIR/log_file.txt
fi
else
echo "BBMap operation on this sample already performed"
fi
cd ${ref_dir}
rm -r ${out_dir}/temp_ops
cd ${SCRIPT_DIR}/CONSULT-II
counter=0
if [ -f "${out_dir}/${direc_name}/consult/unclassified-seq_${genome}_merged" ] && [ "0" -eq "$assembly_counter" ]; then
test_var=0
test_var=`grep "$genome" $SCRIPT_DIR/log_file.txt | grep -c -e "D$" -e "DE$" -e "DEB$" -e "DEBC$"` || true
if [ "1" -eq "$test_var" ]; then
counter=1
else
rm ${out_dir}/${direc_name}/consult/unclassified-seq_${genome}_merged
fi
fi
if [ "0" -eq "$counter" ] && [ "0" -eq "$assembly_counter" ]; then
echo "CONSULT-II decontamination step starts"
./consult_search --unclassified-out -i all_nbrhood_kmers_k32_p3l2clmn7_K15-map2-171_ToL/ -q ${out_dir}/${direc_name}/bbmap/${genome}_merged.fq -o ${out_dir}/${direc_name}/consult/
echo "CONSULT-II decontamination step ends"
var=`grep "$genome" $SCRIPT_DIR/log_file.txt`
if [ "1" -eq "$interleaven_counter" ]; then
var1="$genome""IAD"
sed -i "s/$var/$var1/" $SCRIPT_DIR/log_file.txt
else
var1="$genome""AD"
sed -i "s/$var/$var1/" $SCRIPT_DIR/log_file.txt
fi
else
echo "CONSULT-II decontamination step on this sample already performed"
fi
cd ${SCRIPT_DIR}/kraken2
counter=0
if [ -f "${out_dir}/${direc_name}/kraken/unclassified-kra_${genome}.fq" ] && [ "0" -eq "$assembly_counter" ]; then
test_var=0
test_var=`grep "$genome" $SCRIPT_DIR/log_file.txt | grep -c -e "E$" -e "EB$" -e "EBC$"` || true
if [ "1" -eq "$test_var" ]; then
counter=1
else
rm ${out_dir}/${direc_name}/kraken/unclassified-kra_${genome}.fq
fi
fi
if [ "0" -eq "$counter" ] && [ "0" -eq "$assembly_counter" ]; then
echo "Kraken2 decontamination step starts"
./kraken2 --db krakenlib/ ${out_dir}/${direc_name}/consult/unclassified-seq_${genome}_merged --unclassified-out ${out_dir}/${direc_name}/kraken/unclassified-kra_${genome}.fq
echo "Kraken2 decontamination step ends"
var=`grep "$genome" $SCRIPT_DIR/log_file.txt`
if [ "1" -eq "$interleaven_counter" ]; then
var1="$genome""IADE"
sed -i "s/$var/$var1/" $SCRIPT_DIR/log_file.txt
else
var1="$genome""ADE"
sed -i "s/$var/$var1/" $SCRIPT_DIR/log_file.txt
fi
else
echo "Kraken2 decontamination step on this sample already performed"
fi
f=`ls ${lib_dir} | wc -l`
mkdir -p ${out_dir}/temp_ops
cd ${out_dir}/temp_ops
counter=0
if [ -d "${lib_dir}/unclassified-kra_${genome}" ] || [ -d "${lib_dir}/${genome}" ]; then
test_var=0
test_var=`grep "$genome" $SCRIPT_DIR/log_file.txt | grep -c -e "B$" -e "BC$"` || true
if [ "1" -eq "$test_var" ]; then
counter=1
else
rm -r ${lib_dir}/unclassified-kra_${genome} || true
rm -r ${lib_dir}/${genome} || true
fi
fi
if [ "0" -eq "$counter" ]; then
if [ "0" -eq "$assembly_counter" ]; then
${SCRIPT_DIR}/skmer_pipeline.sh $f ${out_dir}/${direc_name}/kraken unclassified-kra_${genome}.fq $lib_dir $cores
else
if [ "$extension_1" = "gz" ]; then
${SCRIPT_DIR}/skmer_pipeline.sh $f ${out_dir}/${direc_name}/assemblies ${genome}.fna $lib_dir $cores
else
${SCRIPT_DIR}/skmer_pipeline.sh $f ${input} ${input_1} $lib_dir $cores
fi
fi
if [ "1" -eq "$interleaven_counter" ]; then
var=`grep "$genome" $SCRIPT_DIR/log_file.txt`
var1="$genome""IADEB"
sed -i "s/$var/$var1/" $SCRIPT_DIR/log_file.txt
elif [ "1" -eq "$assembly_counter" ]; then
echo "$genome""B">>$SCRIPT_DIR/log_file.txt
else
var=`grep "$genome" $SCRIPT_DIR/log_file.txt`
var1="$genome""ADEB"
sed -i "s/$var/$var1/" $SCRIPT_DIR/log_file.txt
fi
else
echo "Skmer operation on this sample already performed"
fi
cd ${ref_dir}
rm -r ${out_dir}/temp_ops
if [ -d "${lib_dir}/unclassified-kra_${genome}" ]; then
cov_val=$(grep coverage ${lib_dir}/unclassified-kra_${genome}/unclassified-kra_${genome}.dat |cut -f2)
else
cov_val=0
fi
counter=0
if [ -d "${out_dir}/${direc_name}/respect/${genome}" ]; then
test_var=0
test_var=`grep "$genome" $SCRIPT_DIR/log_file.txt | grep -c "C$"` || true
if [ "1" -eq "$test_var" ]; then
counter=1
else
rm -r ${out_dir}/${direc_name}/respect/${genome}
fi
fi
mkdir -p ${out_dir}/${direc_name}/respect/${genome}/output/tmp
if [ "0" -eq "$counter" ]; then
if [ "0" -eq "$assembly_counter" ]; then
${SCRIPT_DIR}/respect_pipeline.sh $cov_val $genome $lib_dir ${out_dir}/${direc_name} $iterations $threads $assembly_counter $extension_1 ${out_dir}/${direc_name}
else
if [ "$extension_1" = "gz" ]; then
${SCRIPT_DIR}/respect_pipeline.sh $cov_val $genome $lib_dir ${out_dir}/${direc_name} $iterations $threads $assembly_counter $extension_1 ${out_dir}/${direc_name}
else
${SCRIPT_DIR}/respect_pipeline.sh $cov_val $genome $lib_dir ${input} $iterations $threads $assembly_counter $extension_1 ${out_dir}/${direc_name}
fi
fi
var=`grep "$genome" $SCRIPT_DIR/log_file.txt`
if [ "1" -eq "$interleaven_counter" ]; then
var1="$genome""IADEBC"
sed -i "s/$var/$var1/" $SCRIPT_DIR/log_file.txt
elif [ "1" -eq "$assembly_counter" ]; then
var1="$genome""BC"
sed -i "s/$var/$var1/" $SCRIPT_DIR/log_file.txt
else
var1="$genome""ADEBC"
sed -i "s/$var/$var1/" $SCRIPT_DIR/log_file.txt
fi
else
echo "Respect operation on this sample already performed"
fi
done
echo "Skmer distance running"
skmer distance ${lib_dir}
echo "Skmer distance complete"
echo "Post processing starts"
${SCRIPT_DIR}/post_processing_pipeline.sh ${SCRIPT_DIR} ${ref_dir} ${direc_name} ${lib_dir}
echo "Post processing complete"
conda deactivate