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launch_universc.sh
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#!/bin/sh
# UniverSC
# Copyright (C) 2019 Tom Kelly; Kai Battenberg
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
install=false
######UniverSC version#####
universcversion="1.0.2"
##########
#####locate cellranger and get cellranger version#####
cellrangerpath=$(which cellranger) #location of Cell Ranger
if [[ -z $cellrangerpath ]]; then
echo "cellranger command is not found."
exit 1
fi
## detects version by attempting to parse "cellranger --version" (older versions do not support this by print the help header if invalid args given)
cellrangerversion=$(cellranger --version 2>/dev/null | head -n 2 | tail -n 1 | rev | cut -f1 -d" " | rev | cut -f2 -d'(' | cut -f1 -d')')
if [[ $verbose ]]; then
echo $cellrangerversion
fi
##########
#####locate launch_universc.sh, barcode sources, and other tools######
SOURCE="${BASH_SOURCE[0]}"
SDIR=""
RDIR=""
while [[ -h "$SOURCE" ]]; do #resolve $SOURCE until the file is no longer a symlink
TARGET="$(readlink "$SOURCE")"
if [[ $TARGET == /* ]]; then
echo "SOURCE '$SOURCE' is an absolute symlink to '$TARGET'"
SOURCE="$TARGET"
else
SDIR="$( dirname "$SOURCE" )"
echo "SOURCE '$SOURCE' is a relative symlink to '$TARGET' (relative to '$SDIR')"
SOURCE="$SDIR/$TARGET" #if $SOURCE is a relative symlink, we need to resolve it relative to the path where the symlink file was located
fi
done
SDIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
RDIR="$( dirname "$SOURCE" )"
if [[ $RDIR != $SDIR ]]; then
echo "'$RDIR' resolves to '$SDIR'"
fi
echo "Running launch_universc.sh in '$SDIR'"
TOOLS=${SDIR}/sub
BARCODERECOVER=${TOOLS}/RecoverBarcodes.pl
MAKEINDROPBARCODES=${TOOLS}/MakeIndropBarcodes.pl
PERCELLSTATS=${TOOLS}/ExtractBasicStats.pl
##########
#####define set options#####
lockfile=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/.lock #path for .lock file
lastcallfile=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/.last_called #path for .last_called
lastcall=`[[ -e $lastcallfile ]] && cat $lastcallfile || echo ""`
lastcall_b=`echo ${lastcall} | cut -f1 -d' '`
lastcall_u=`echo ${lastcall} | cut -f2 -d' '`
lastcall_p=`echo ${lastcall} | cut -f3 -d' '`
barcodedir=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes #folder within cellranger with the whitelist barcodes
if [[ $(echo "${cellrangerversion} 4.0.0" | tr " " "\n" | sort -V | tail -n 1) == ${cellrangerversion} ]]; then
barcodedir=$(dirname $cellrangerpath)/lib/python/cellranger/barcodes
mkdir -p ${cellrangerpath}-cs/${cellrangerversion}
ln -sf $(dirname $cellrangerpath)/mro/rna ${cellrangerpath}-cs/${cellrangerversion}/mro
ln -sf $(dirname $cellrangerpath)/lib ${cellrangerpath}-cs/${cellrangerversion}/lib
fi
barcodefile=""
crIN=input4cellranger #name of the directory with all FASTQ and index files given to Cell Ranger
whitelistdir=${SDIR}/whitelists #path to whitelists
whitelistfile="outs/whitelist.txt" #name of the whitelist file added to the cellranger output
percellfile="outs/basic_stats.txt" #name of the file with the basic statistics of the run added to the cellranger output
##########
#####checking if Universc and Cell Ranger are writable#####
#Cell Ranger
if ! [[ -w "$barcodedir" ]]; then
echo "Error: Trying to run Cell Ranger installed at ${cellrangerpath}"
echo "launch_universc.sh can only run with Cell Ranger installed locally"
echo "Install Cell Ranger in a directory with write permissions such as /home/`whoami`/local and export to the PATH"
echo "The following versions of Cell Ranger are found:"
echo " `whereis cellranger`"
exit 1
fi
#convert
if ! [[ -w "$SDIR" ]]; then
echo "Error: Trying to run launch_universc.sh installed at $SDIR"
echo "$SDIR must be writable to run launch_universc.sh"
echo "Install launch_universc.sh in a directory with write permissions such as /home/`whoami`/local and export to the PATH"
exit 1
fi
##########
#####usage statement#####
## detect shell across different OS
if [[ -z $VENDOR ]]; then
if [[ $(uname -a | grep "[Mm]ac") ]]; then
VENDOR="apple"
else
VENDOR="linux"
fi
fi
if [[ $VENDOR != "apple" ]]; then
SHELL=$(readlink -f /proc/$$/exe | cut -d'/' -f3)
else
SHELL=$(ps -p $$ | awk '$1 == PP {print $4}' PP=$$)
fi
## detect how called (e.g., bash converrt.sh or ./launch_universc.sh)
if [[ $(which launch_universc.sh) == *"/"* ]] || [[ $0 == *"/"* ]]; then
SHELL=''
invocation=$0
else
if [[ ! -z $ZSH_VERSION ]]; then
SHELL="zsh"
elif [[ ! -z $KSH_VERSION ]]; then
SHELL="ksh"
elif [[ ! -z $FISH_VERSION ]]; then
SHELL="fish"
elif [[ ! -z $BASH_VERSION ]]; then
SHELL="bash"
else
SHELL=$SHELL
fi
invocation=$(echo $(basename $0))
fi
if [[ $SHELL != "" ]]; then
SHELL=" $SHELL"
fi
copyright="
UniverSC Copyright (C) 2019 Tom Kelly; Kai Battenberg
"
notice="
This program comes with ABSOLUTELY NO WARRANTY; for details type 'cat LICENSE'.
This is free software, and you are welcome to redistribute it
under certain conditions; type 'cat LICENSE' for details.
"
disclaimer="
Cell Ranger is called as third-party dependency and is not maintained
by this project. Please ensure you comply with the End User License
Agreement for all software installed where applicable; for details type 'cat README.md'.
"
help='
Usage:
'$SHELL' '$invocation' --testrun -t TECHNOLOGY
'$SHELL' '$invocation' -t TECHNOLOGY --setup
'$SHELL' '$invocation' -R1 FILE1 -R2 FILE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]
'$SHELL' '$invocation' -R1 READ1_LANE1 READ1_LANE2 -R2 READ2_LANE1 READ2_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]
'$SHELL' '$invocation' -f SAMPLE_LANE -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]
'$SHELL' '$invocation' -f SAMPLE_LANE1 SAMPLE_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]
'$SHELL' '$invocation' -v
'$SHELL' '$invocation' -h
Convert sequencing data (FASTQ) from Nadia or ICELL8 platforms for compatibility with 10x Genomics and run cellranger count
Mandatory arguments to long options are mandatory for short options too.
--testrun Initiates a test trun with the test dataset
-R1, --read1 FILE Read 1 FASTQ file to pass to Cell Ranger (cell barcodes and umi)
-R2, --read2 FILE Read 2 FASTQ file to pass to Cell Ranger
-I1, --index1 FILE Index (I1) FASTQ file to pass to Cell Ranger (OPTIONAL)
-I2, --index2 FILE Index (I2) FASTQ file to pass to Cell Ranger (OPTIONAL and EXPERIMENTAL)
-f, --file NAME Path and the name of FASTQ files to pass to Cell Ranger (prefix before R1 or R2)
e.g. /path/to/files/Example_S1_L001
-i, --id ID A unique run id, used to name output folder
-d, --description TEXT Sample description to embed in output files.
-r, --reference DIR Path of directory containing 10x-compatible reference.
-t, --technology PLATFORM Name of technology used to generate data.
Supported technologies:
10x Genomics (version automatically detected): 10x, chromium
10x Genomics version 2 (16bp barcode, 10bp UMI): 10x-v2, chromium-v2
10x Genomics version 3 (16bp barcode, 12bp UMI): 10x-v3, chromium-v3
CEL-Seq (8bp barcode, 4bp UMI): celseq
CEL-Seq2 (6bp UMI, 6bp barcode): celseq2
Drop-Seq (12bp barcode, 8bp UMI): nadia, dropseq
ICELL8 version 3 (11bp barcode, 14bp UMI): icell8 or custom
inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1
inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2
MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1
MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2
Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384
Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536
SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq
SeqWell (12bp barcode, 8bp UMI): seqwell
Smart-seq, Smart-seq2 (16bp barcode, No UMI): smartseq2
Smart-seq2-UMI, Smart-seq3 (16bp barcode, 8bp UMI): smartseq3
SPLiT-Seq (10bp UMI, 18bp barcode): splitseq
SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad
Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
e.g. Custom (16bp barcode, 10bp UMI): custom_16_10
Experimental technologies (not yet supported):
inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
Sci-Seq (8bp UMI, 22bp barcode): sciseq
-b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode)
-c, --chemistry CHEM Assay configuration, autodetection is not possible for converted files: 'SC3Pv2' (default), 'SC5P-PE', or 'SC5P-R2'
-n, --force-cells NUM Force pipeline to use this number of cells, bypassing the cell detection algorithm.
-j, --jobmode MODE Job manager to use. Valid options: 'local' (default), 'sge', 'lsf', or a .template file
--localcores NUM Set max cores the pipeline may request at one time.
Only applies when --jobmode=local.
--localmem NUM Set max GB the pipeline may request at one time.
Only applies when --jobmode=local.
--mempercore NUM Set max GB each job may use at one time.
Only applies in cluster jobmodes.
-p, --per-cell-data Generates a file with basic run statistics along with per-cell data
--setup Set up whitelists for compatibility with new technology and exit
--as-is Skips the FASTQ file conversion if the file already exists
-h, --help Display this help and exit
-v, --version Output version information and exit
--verbose Print additional outputs for debugging
For each fastq file, follow the naming convention below:
<SampleName>_<SampleNumber>_<LaneNumber>_<ReadNumber>_001.fastq
e.g. EXAMPLE_S1_L001_R1_001.fastq
Example_S4_L002_R2_001.fastq.gz
For custom barcode and umi length, follow the format below:
custom_<barcode>_<UMI>
e.g. custom_16_10 (which is the same as 10x)
Files will be renamed if they do not follow this format. File extension will be detected automatically.
'
echo $copyright
echo $notice
echo $disclaimer
if [[ -z $@ ]]; then
echo "$help"
exit 1
fi
##########
#####options#####
#variable options
setup=false
convert=true
testrun=false
read1=()
read2=()
index1=()
index2=()
SAMPLE=""
LANE=()
id=""
description=""
reference=""
ncells=""
chemistry=""
jobmode="local"
ncores=""
mem=""
percelldata=false
next=false
for op in "$@"; do
if $next; then
next=false;
continue;
fi
case "$op" in
--testrun)
testrun=true
next=false
shift
;;
-R1|--read1)
shift
if [[ "$1" != "" ]]; then
arg=$1
while [[ ! "$arg" == "-"* ]] && [[ "$arg" != "" ]]; do
read1+=("${1/%\//}")
shift
arg=$1
done
next=true
elif [[ -z $read1 ]]; then
echo "Error: file input missing for --read1"
exit 1
fi
;;
-R2|--read2)
shift
if [[ "$1" != "" ]]; then
arg=$1
while [[ ! "$arg" == "-"* ]] && [[ "$arg" != "" ]]; do
read2+=("${1/%\//}")
shift
arg=$1
done
next=true
elif [[ -z $read2 ]]; then
echo "Error: file input missing for --read2"
exit 1
fi
;;
-I1|--index1|--index)
shift
if [[ "$1" != "" ]]; then
arg=$1
while [[ ! "$arg" == "-"* ]] && [[ "$arg" != "" ]]; do
index1+=("${1/%\//}")
shift
arg=$1
done
next=true
elif [[ -z $index1 ]]; then
echo "Error: file input missing for --index1"
exit 1
fi
;;
-I2|--index2)
shift
if [[ "$1" != "" ]]; then
arg=$1
while [[ ! "$arg" == "-"* ]] && [[ "$arg" != "" ]]; do
index2+=("${1/%\//}")
shift
arg=$1
done
next=true
elif [[ -z $index1 ]]; then
echo "Error: file input missing for --index1"
exit 1
fi
;;
-f|--file)
shift
if [[ "$1" != "" ]]; then
arg=$1
while [[ ! "$arg" == "-"* ]] && [[ "$arg" != "" ]]; do
read1+=("${1}_R1_001")
read2+=("${1}_R2_001")
shift
arg=$1
done
skip=true
else
echo "Error: file input missing for --file"
exit 1
fi
;;
-i|--id)
shift
if [[ "$1" != "" ]]; then
id="${1/%\//}"
next=true
shift
else
echo "Error: value missing for --id"
exit 1
fi
;;
-d|--description)
shift
if [[ "$1" != "" ]]; then
description="${1/%\//}"
next=true
shift
else
echo "Error: value missing for --description"
exit 1
fi
;;
-r|--reference)
shift
if [[ "$1" != "" ]]; then
reference="${1/%\//}"
next=true
shift
else
echo "Error: value missing for --reference: reference transcriptome generated by cellranger mkfastq required"
exit 1
fi
;;
-t|--technology)
shift
if [[ $1 != "" ]]; then
technology="${1/%\//}"
technology=`echo "$technology" | tr '[:upper:]' '[:lower:]'`
next=true
shift
else
echo "Error: value missing for --technology"
exit 1
fi
;;
-b|--barcodefile)
shift
if [[ "$1" != "" ]]; then
barcodefile="${1/%\//}"
next=true
shift
else
echo "Error: value missing for --barcodefile"
exit 1
fi
;;
-c|--chemistry)
shift
if [[ "$1" != "" ]]; then
chemistry="${1/%\//}"
next=true
shift
else
echo "Error: value missing for --chemistry"
exit 1
fi
;;
-n|--force-cells)
shift
if [[ "$1" != "" ]]; then
ncells="${1/%\//}"
next=true
shift
else
echo "Error: value missing for --force-cells"
exit 1
fi
;;
-j|--jobmode)
shift
if [[ "$1" != "" ]]; then
jobmode="${1/%\//}"
next=true
shift
else
echo "Error: value missing for --jobmode"
exit 1
fi
;;
--localcores)
shift
if [[ "$1" != "" ]]; then
ncores="${1/%\//}"
next=true
shift
else
echo "Error: value missing for --localcores"
exit 1
fi
;;
--localmem)
shift
if [[ "$1" != "" ]]; then
mem="${1/%\//}"
next=true
shift
else
echo "Error: value missing for --localmem"
exit 1
fi
;;
--mempercore)
shift
if [[ "$1" != "" ]]; then
mem="${1/%\//}"
next=true
shift
else
echo "Error: value missing for --mempercore"
exit 1
fi
;;
-p|--per-cell-data)
percelldata=true
next=false
shift
;;
--setup)
setup=true
next=false
shift
;;
--as-is)
convert=false
next=false
shift
;;
-h|--help)
echo "$help"
exit 0
;;
-v|--version)
echo "launch_universc.sh version ${universcversion}"
echo "cellranger version ${cellrangerversion}"
exit 0
;;
--verbose)
echo "debugging mode activated"
verbose=true
next=false
shift
;;
-*)
echo "Error: Invalid option: $op"
exit 1
;;
esac
done
##########
#####check if this is a test run#####
if [[ $testrun == "true" ]]; then
if [[ ${#read1[@]} -gt 0 ]] || [[ ${#read2[@]} -gt 0 ]]; then
echo "Error: for test run, no R1 or R2 file can be selected."
exit 1
elif [[ -n $reference ]]; then
echo "Error: for test run, reference will be set automatically."
exit 1
elif [[ -n $id ]]; then
echo "Error: for test run, id will be set automatically."
exit 1
fi
TESTDIR=${SDIR}/test
reference=${TESTDIR}/cellranger_reference/cellranger-tiny-ref/3.0.0
id=test-tiny-${technology}
description=${id}
percelldata=true
if [[ $technology == "10x" ]]; then
gunzip -fk ${TESTDIR}/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L00[12]_R[12]_001.fastq.gz
read1=("${TESTDIR}/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_001.fastq" "${TESTDIR}/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R1_001.fastq")
read2=("${TESTDIR}/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R2_001.fastq" "${TESTDIR}/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R2_001.fastq")
index1=("${TESTDIR}/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_I1_001.fastq.gz" "${TESTDIR}/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_I1_001.fastq.gz")
elif [[ $technology == "nadia" ]]; then
gunzip -fk ${TESTDIR}/shared/dropseq-test/SRR1873277_S1_L001_R[12]_001.fastq.gz
read1=("${TESTDIR}/shared/dropseq-test/SRR1873277_S1_L001_R1_001.fastq")
read2=("${TESTDIR}/shared/dropseq-test/SRR1873277_S1_L001_R2_001.fastq")
elif [[ $technology == "icell8" ]]; then
gunzip -fk ${TESTDIR}/shared/icell8-test/ICELL8_01_S1_L00[12]_R[12]_001.fastq.gz
read1=("${TESTDIR}/shared/icell8-test/ICELL8_01_S1_L001_R1_001.fastq" "${TESTDIR}/shared/icell8-test/ICELL8_01_S1_L002_R1_001.fastq")
read2=("${TESTDIR}/shared/icell8-test/ICELL8_01_S1_L001_R2_001.fastq" "${TESTDIR}/shared/icell8-test/ICELL8_01_S1_L002_R2_001.fastq")
barcodefile=${TESTDIR}/shared/icell8-test/BarcodeList.txt
ncells=`wc -l $barcodefile | cut -f1 -d' '`
else
echo "Error: for test run, -t needs to be 10x, nadia, or icell8"
exit 1
fi
fi
##########
#####Check if technology matches expected inputs#####
if [[ $verbose ]]; then
echo " checking option: --technology"
fi
if [[ "$technology" == "10x" ]] || [[ "$technology" == "chromium" ]]; then
technology="10x"
elif [[ "$technology" == "10x-v2" ]] || [[ "$technology" == "chromium-v2" ]]; then
technology="10x-v2"
elif [[ "$technology" == "10x-v3" ]] || [[ "$technology" == "chromium-v3" ]]; then
technology="10x-v3"
elif [[ "$technology" == "celseq" ]] || [[ "$technology" == "cel-seq" ]]; then
technology="celseq"
elif [[ "$technology" == "celseq2" ]] || [[ "$technology" == "cel-seq2" ]]; then
technology="celseq2"
elif [[ "$technology" == "nadia" ]] || [[ "$technology" == "dropseq" ]] || [[ "$technology" == "drop-seq" ]]; then
technology="nadia"
elif [[ "$technology" == "icell8" ]] || [[ "$technology" == "icell-8" ]]; then
technology="icell8"
elif [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrops-v1" ]] || [[ "$technology" == "indropv1" ]] || [[ "$technology" == "indropsv1" ]] || [[ "$technology" == "1cellbio-v1" ]] || [[ "$technology" == "1cellbiov1" ]]; then
technology="indrop-v1"
elif [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrops-v2" ]] || [[ "$technology" == "indropv2" ]] || [[ "$technology" == "indropsv2" ]] || [[ "$technology" == "1cellbio-v2" ]] || [[ "$technology" == "1cellbiov2" ]]; then
technology="indrop-v2"
elif [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "indrops-v3" ]] || [[ "$technology" == "indropv3" ]] || [[ "$technology" == "indropsv3" ]] || [[ "$technology" == "1cellbio-v3" ]] || [[ "$technology" == "1cellbiov3" ]]; then
technology="indrop-v3"
elif [[ "$technology" == "marsseq" ]] || [[ "$technology" == "mars-seq" ]] || [[ "$technology" == "marsseq-v1" ]] || [[ "$technology" == "mars-seq-v1" ]] || [[ "$technology" == "marsseqv1" ]] || [[ "$technology" == "mars-seqv1" ]]; then
technology="marsseq-v1"
elif [[ "$technology" == "marsseq2" ]] || [[ "$technology" == "mars-seq2" ]] || [[ "$technology" == "marsseq-v2" ]] || [[ "$technology" == "mars-seq-v2" ]] || [[ "$technology" == "marsseqv2" ]] || [[ "$technology" == "mars-seqv2" ]]; then
technology="marsseq-v2"
elif [[ "$technology" == "quartz-seq2-384" ]] || [[ "$technology" == "quartzseq2-384" ]] || [[ "$technology" == "quartz-seq2-v3.1" ]] || [[ "$technology" == "quartzseq2-v3.1" ]] || [[ "$technology" == "quartzseq2v3.1" ]]; then
technology="quartz-seq2-384"
elif [[ "$technology" == "quartz-seq2-1536" ]] || [[ "$technology" == "quartzseq2-1536" ]] || [[ "$technology" == "quartz-seq2-v3.2" ]] || [[ "$technology" == "quartzseq2-v3.2" ]] || [[ "$technology" == "quartzseq2v3.2" ]]; then
technology="quartz-seq2-1536"
elif [[ "$technology" == "sciseq" ]] || [[ "$technology" == "sci-seq" ]]; then
technology="sciseq"
elif [[ "$technology" == "scrbseq" ]] || [[ "$technology" == "scrb-seq" ]] || [[ "$technology" == "mcscrbseq" ]] || [[ "$technology" == "mcscrb-seq" ]]; then
technology="scrbseq"
elif [[ "$technology" == "seqwell" ]] || [[ "$technology" == "seq-well" ]]; then
technology="seqwell"
elif [[ "$technology" == "smartseq" ]] || [[ "$technology" == "smart-seq" ]] || [[ "$technology" == "smartseq2" ]] || [[ "$technology" == "smart-seq2" ]]; then
technology="smartseq2"
nonUMI=true
elif [[ "$technology" == "smartseq2-umi" ]] || [[ "$technology" == "smart-seq2-umi" ]]; then
technology="smartseq2-umi"
nonUMI=false
elif [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "smart-seq3" ]]; then
technology="smartseq3"
nonUMI=false
elif [[ "$technology" == "splitseq" ]] || [[ "$technology" == "split-seq" ]]; then
technology="splitseq"
elif [[ "$technology" == "surecell" ]] || [[ "$technology" == "surecellseq" ]] || [[ "$technology" == "surecell-seq" ]] || [[ "$technology" == "ddseq" ]] || [[ "$technology" == "dd-seq" ]] || [[ "$technology" == "bioraad" ]]; then
technology="surecell"
elif [[ "$technology" == "custom"* ]]; then
fields=$((`echo $technology | grep -o "_" | wc -l`+1))
if [[ $fields -ne 3 ]]; then
echo "Error: custom input must have exactly 3 fields separated by '_', e.g. custom_10_16"
else
b=`echo $technology | cut -f2 -d'_'`
u=`echo $technology | cut -f3 -d'_'`
if ! [[ "$b" =~ ^[0-9]+$ ]] || ! [[ "$u" =~ ^[0-9]+$ ]]; then
echo "Error: option -t needs to be a technology listed or custom_<barcode>_<UMI>"
exit 1
fi
setup=true
fi
else
echo "Error: option -t needs to be a technology listed or custom_<barcode>_<UMI>"
exit 1
fi
if [[ $verbose ]]; then
echo " technology set to ${technology}"
fi
if [[ "$technology" == "icell8" ]]; then
echo "***WARNING: ${technology} should only be used for kits that have valid UMIs***"
fi
if [[ "$technology" == "smartseq" ]] || [[ "$technology" == "smartseq2-umi" ]] || [[ "$technology" == "smartseq3" ]]; then
echo "***WARNING: ${technology} should only be used for kits that have UMIs***"
echo "... UMI reads will be filtered using a tag sequence which will be removed"
echo "... barcodes will derived from dual indexes"
fi
if [[ "$technology" == "smartseq2" ]] || [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrop-v3" ]]; then
echo "***Note: launch_universc.sh support for barcodes in dual indexes is experimental. Make sure that samples are demultiplexed prior to running launch_universc.sh***"
fi
##########
#####Setting barcode and UMI length according to the set technology#####
if [[ $verbose ]]; then
echo " setting barcode and UMI lengths for ${technology}"
fi
#barcode and umi lengths given by options
barcodelength=""
if [[ $verbose ]]; then
echo "barcodelength before $barcodelength"
fi
umilength=""
minlength=""
if [[ "$technology" == "10x" ]]; then
barcodelength=16
umilength=10
minlength=16
elif [[ "$technology" == "10x-v2" ]]; then
barcodelength=16
umilength=10
minlength=16
elif [[ "$technology" == "10x-v3" ]]; then
barcodelength=16
umilength=12
minlength=16
elif [[ "$technology" == "celseq" ]]; then
barcodelength=8
umilength=4
minlength=8
elif [[ "$technology" == "celseq2" ]]; then
barcodelength=6
umilength=6
minlength=6
elif [[ "$technology" == "nadia" ]]; then
barcodelength=12
umilength=8
minlength=12
elif [[ "$technology" == "icell8" ]]; then
barcodelength=11
umilength=14
minlength=11
elif [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrop-v2" ]]; then
barcodelength=19
umilength=6
minlength=16
elif [[ "$technology" == "indrop-v3" ]]; then
barcodelength=16
umilength=6
minlength=16
elif [[ "$technology" == "marsseq-v1" ]]; then
barcodelength=6
umilength=10
minlength=6
elif [[ "$technology" == "marsseq-v2" ]]; then
barcodelength=7
umilength=8
minlength=7
elif [[ "$technology" == "quartz-seq2-384" ]]; then
barcodelength=14
umilength=8
minlength=14
elif [[ "$technology" == "quartz-seq2-1536" ]]; then
barcodelength=15
umilength=8
minlength=15
elif [[ "$technology" == "sciseq" ]]; then
barcodelength=22
umilength=8
minlength=22
elif [[ "$technology" == "scrbseq" ]]; then
barcodelength=6
umilength=10
minlength=6
elif [[ "$technology" == "seqwell" ]]; then
barcodelength=8
umilength=12
minlength=8
elif [[ "$technology" == "smartseq2" ]]; then
barcodelength=16
umilength=8
minlength=16
elif [[ "$technology" == "smartseq3" ]]; then
barcodelength=16
umilength=8
minlength=16
elif [[ "$technology" == "splitseq" ]]; then
barcodelength=18
umilength=10
minlength=18
elif [[ "$technology" == "surecell" ]]; then
barcodelength=18
umilength=8
minlength=18
elif [[ "$technology" == "custom"* ]]; then
barcodelength=`echo $technology | cut -f2 -d'_'`
umilength=`echo $technology | cut -f3 -d'_'`
minlength=${barcodelength}
fi
if [[ $minlength -gt 16 ]]; then
minlength=16
fi
if [[ $verbose ]]; then
echo " barcode and UMI lengths set as ${barcodelength} and ${umilength} respectively"
fi
##########
#####Setting chemistry#####
#check if chemistry matches expected inputs
if [[ $verbose ]]; then
echo " checking option: --chemistry"
fi
if [[ -n $chemistry ]]; then
if [[ "$chemistry" != "auto" ]] && \
[[ "$chemistry" != "threeprime" ]] && \
[[ "$chemistry" != "fiveprime" ]] && \
[[ "$chemistry" != "SC3Pv1" ]] && \
[[ "$chemistry" != "SC3Pv2" ]] && \
[[ "$chemistry" != "SC3Pv3" ]] && \
[[ "$chemistry" != "SC5P-PE" ]] && \
[[ "$chemistry" != "SC5P-R2" ]] && \
[[ "$chemistry" != "SC-FB" ]]; then
echo "Error: option -c can be auto, threeprime, fiveprime, SC3Pv1, SC3Pv2, SC3Pv3, SC5P-PE, SC5P-R2, or SC-FB"
exit 1
fi
fi
#determine what chemistry is recommended
temp_chemistry="SC3Pv2"
if [[ $umilength -gt 10 ]]; then
temp_chemistry="SC3Pv3"
fi
if [[ "$technology" == "smartseq" ]] || [[ "$technology" == "smartseq3" ]];then
temp_chemistry="SC5P-PE"
fi
if [[ "$technology" == "10x" ]]; then
temp_chemistry="auto"
fi
#set chemistry
if [[ -z ${chemistry} ]]; then
chemistry=${temp_chemistry}
elif [[ "$chemistry" != "$temp_chemistry" ]]; then
echo "***WARNING: chemistry is set to ${chemistry} where ${temp_chemistry} would have been chosen automatically. proceed with caution.***"
fi
#set default barcode and umi lengths
barcode_default=16
umi_default=10
if [[ "$chemistry" == "SC3Pv3" ]]; then
umi_default=12
fi
totallength=`echo $((${barcode_default}+${umi_default}))`
#adjustment lengths
if [[ $verbose ]]; then
echo "barcode length: $barcodelength"
echo "barcode default: $barcode_default"
fi
barcodeadjust=`echo $(($barcodelength-$barcode_default))`
umiadjust=`echo $(($umilength-$umi_default))`
if [[ $verbose ]]; then
echo "barcode adjust: $barcodeadjust "
fi
if [[ $verbose ]]; then
echo " chemistry set to ${chemistry}"
fi
##########
#####Input file curation 1: Check if number of R1, R2, I1, and I2 files are as expected#####
#get unique inputs
read1=(`echo "${read1[@]}" | tr ' ' '\n' | sort -u | tr '\n' ' '`)
read2=(`echo "${read2[@]}" | tr ' ' '\n' | sort -u | tr '\n' ' '`)
index1=(`echo "${index1[@]}" | tr ' ' '\n' | sort -u | tr '\n' ' '`)
index2=(`echo "${index2[@]}" | tr ' ' '\n' | sort -u | tr '\n' ' '`)
#check for presence of read1 and read2 files
if [[ $verbose ]]; then
echo " checking option: --read1 and --read2"
fi
if [[ $setup == "false" ]]; then
if [[ ${#read1[@]} -eq 0 ]]; then
echo "Error: option --read1 or --file is required"
exit 1
elif [[ ${#read2[@]} -eq 0 ]]; then
echo "Error: option --read2 or --file is required"
exit 1
fi
fi
#check for presence of index files
if [[ $verbose ]]; then
echo " checking option: --index1 and --index2"
fi
#index 1
if [[ $setup == "false" ]]; then
if [[ ${#index1[@]} -ne ${#read1[@]} ]]; then
if [[ ${#index1[@]} -gt 0 ]]; then
echo " Error: number of index1 files is not matching the number of R1 and R2 files"
echo " either give no index1 file, or give index1 file for each and every read1 file"
exit 1
else
if [[ $verbose ]]; then
echo " No index files given. Automatically detecting from R1 and R2 file names..."
fi
r1_list=("${read1[@]}")
r2_list=("${read2[@]}")
i1_list=()
for j in ${!r1_list[@]}; do
read=${r1_list[$j]}
R1_file=$read
if [[ $read == *R1* ]]; then
R2_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R2/' )
R4_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R4/' )
I1_file=$(echo $read | perl -pne 's/(.*)_R1/$1_I1/' )
if [[ -f $R4_file ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R4_file})'*.gz') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R4_file})'*.fastq') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R4_file})'*.fq') ]]; then
if [[ $verbose ]]; then
echo " file $R4_file found, replacing $R1_file ..."
fi
r1_read=$R4_file
r1_list[$j]=$r1_read
if [[ $verbose ]]; then
echo " file $R1_file found, replacing $R2_file ..."
fi
r2_read=$R1_file
r2_list[$j]=$r2_read
if [[ $verbose ]]; then
echo " file $R2_file found, replacing $I1_file ..."
fi
i1_read=$R2_file
i1_list[$j]=$i1_read
fi
if [[ -f $I1_file ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I1_file})'*.gz') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I1_file})'*.fastq') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I1_file})'*.fq') ]]; then
if [[ $verbose ]]; then
echo " file $I1_file found..."
fi
i1_read=$I1_file
i1_list[$j]=$i1_read
fi
fi
done
read1=("${r1_list[@]}")
read2=("${r2_list[@]}")
if [[ ${#i1_list[@]} -eq 0 ]]; then
if [[ $verbose ]]; then
echo "No index files found"
fi
else
index1=("${i1_list[@]}")
if [[ $verbose ]]; then
echo " index files found ${#index1[@]} I1s: ${index1[@]}"
fi
fi
fi
fi
fi
#index 2
if [[ $setup == "false" ]]; then
#only check I2 for dual-indexed techniques
if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sci-seq" ]] || [[ "$technology" == "smartseq"* ]]; then
if [[ ${#index2[@]} -ne ${#read1[@]} ]]; then
if [[ ${#index2[@]} -gt 0 ]]; then
echo " Error: number of index1 files is not matching the number of index2 files"
echo " for $technology, either give no index files or give index1 and index2 for each and every read1 and read2 file"
exit 1
else
if [[ $verbose ]]; then
echo " No index files given. Automatically detecting from R1 and R2 file names..."
fi
r1_list=("${read1[@]}")
r2_list=("${read2[@]}")
i2_list=()
for j in ${!r1_list[@]}; do
read=${r1_list[$j]}
R1_file=$read
if [[ $read == *R1* ]]; then
R2_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R2/' )
R3_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R3/' )
I2_file=$(echo $read | perl -pne 's/(.*)_R1/$1_I2/' )
if [[ -f $R3_file ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R3_file})'*.gz') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R3_file})'*.fastq') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R3_file})'*.fq') ]]; then
if [[ $verbose ]]; then
echo " file $R3_file found, replacing $I2_file ..."
fi
i2_read=$R3_file
i2_list[$j]=$i1_read
fi
if [[ -f $I2_file ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'*.gz') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'*.fastq') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'*.fq') ]]; then
if [[ $verbose ]]; then
echo " file $I2_file found..."
fi
i2_read=$I2_file
i2_list[$j]=$i2_read
fi
fi
done
if [[ ${#i2_list[@]} -eq 0 ]]; then
if [[ $verbose ]]; then
echo "Dual index files not found"
fi
else
index2=("${i2_list[@]}")
if [[ $verbose ]]; then
echo " index files found ${#index2[@]} I2s: ${index2[@]}"
fi
fi
fi
fi
elif [[ ${#index2[@]} -gt 0 ]]; then
echo " Error: $technology does not support dual index"
echo " re-run without selecting any files for --index2"
exit 1
fi
fi
if [[ $verbose ]]; then
echo " ${#read1[@]} read1s: ${read1[@]}"
echo " ${#read2[@]} read2s: ${read2[@]}"
if [[ ${#index1[@]} -gt 0 ]]; then