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launch_universc.sh
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launch_universc.sh
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#!/bin/bash
# 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="1.2.7"
##########
#####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 -f 1 -d" " | rev | cut -f 2 -d'(' | cut -f 1 -d')')
if [[ $verbose ]]; then
echo $cellrangerversion
fi
##########
#####locate launch_universc.sh, barcode sources, and other tools######
echo "script running in $(realpath $0)..."
SOURCE=${BASH_SOURCE[0]}
# check if script is started via SLURM or bash (job ID defined in Slurm job)
if [[ -n $SLURM_JOB_ID ]]; then
if [[ $(echo $SLURM_JOB_ID | wc -w) -ge 1 ]]; then
# check the original location through scontrol and $SLURM_JOB_ID
SOURCE=$(scontrol show job $SLURM_JOBID | awk -F= '/Command=/{print $2}')
fi
fi
SDIR=""
RDIR=""
while [[ -h "$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 )"
echo "... script called from ${SDIR}"
RDIR="$( dirname "$SOURCE" )"
if [[ $RDIR != $SDIR ]]; then
echo "'$RDIR' resolves to '$SDIR'"
fi
echo "Running launch_universc.sh in '$SDIR'"
TOOLS=${SDIR}/sub
ADDMOCKUMI=${TOOLS}/AddMockUMI.pl
BARCODERECOVER=${TOOLS}/RecoverBarcodes.pl
MAKEINDROPBARCODES=${TOOLS}/MakeIndropBarcodes.pl
FILTERSMARTSEQREADUMI=${TOOLS}/FilterSmartSeqReadUMI.pl
CONCATENATEBARCODES=${TOOLS}/ConcatenateDualIndexBarcodes.pl
PERCELLSTATS=${TOOLS}/ExtractBasicStats.pl
##########
#####define set options#####
# set defaults to 10x if missing (enables unit testing without warnings)
if [[ -z ${lastcall_b} ]]; then
lastcall_b=16
fi
if [[ -z ${lastcall_u} ]]; then
lastcall_u=10
fi
if [[ -z ${lastcall_p} ]]; then
lastcall_p="default:10x"
fi
lockfile=${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 -f 1 -d' '`
lastcall_u=`echo ${lastcall} | cut -f 2 -d' '`
lastcall_p=`echo ${lastcall} | cut -f 3 -d' '`
barcodedir=${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=${SDIR}/whitelists #path to whitelists
whitelistfile="outs/whitelist.txt" #name of the whitelist file added to the cellranger output
percellfile="outs/basic_stats.txt" #name of the file with the basic statistics of the run added to the cellranger output
##########
#####checking if Universc and Cell Ranger are writable#####
# user configuration
host=$(hostname) # returns host for local run and container ID for docker container
user=$(whoami 2> /dev/null || id -ur) # returns username if defined and user ID if not
#Cell Ranger
if ! [[ -w "$barcodedir" ]]; then
echo "Error: Trying to run Cell Ranger installed at ${cellrangerpath}"
echo "launch_universc.sh can only run with Cell Ranger installed locally"
echo "Install Cell Ranger in a directory with write permissions such as /home/${user}/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/${user}/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/$$/exe | cut -d'/' -f 3)
else
SHELL=$(ps -p $$ | 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.
Available here the human genome and various model species:
https://genomec.gsc.riken.jp/gerg/UniverSC/Premade_references/
-t, --technology PLATFORM Name of technology used to generate data.
Supported technologies:
10x Genomics (version 2 or 3 automatically detected): 10x, chromium
10x Genomics version 1 (14 bp barcode, 10 bp UMI): 10x-v1, chromium-v1
10x Genomics version 2 (16 bp barcode, 10 bp UMI): 10x-v2, chromium-v2
10x Genomics version 3 (16 bp barcode, 12 bp UMI): 10x-v3, chromium-v3
Aligent Bravo B (16 bp barcode, No UMI): aligent, bravo
BD Rhapsody v1 (27 bp barcode, 8 bp UMI): bd-rhapsody
BD Rhapsody v2 enhanced beads (27 bp barcode, 8 bp UMI): bd-rhapsody-v2
C1 Fluidigm (16 bp barcode, No UMI): c1, fluidgm-c1
C1 CAGE (16 bp, No UMI): c1-cage
C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq
CEL-Seq (8 bp barcode, 4 bp UMI): celseq
CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2
Drop-Seq (12 bp barcode, 8 bp UMI): dropseq, nadia
ICELL8 3\′ scRNA version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2
ICELL8 3\′ scRNA version 3 (11 bp barcode, 14 bp UMI): icell8
ICELL8 5\′ scRNA with TCR OR kit (10bp barcode, NO bp UMI): icell8-5-prime
ICELL8 full-length scRNA with Smart-Seq (16 bp barcode, No UMI): icell8-full-length
inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1
inDrops version 2 (19 bp barcode, 6 bp UMI): indrops-v2, 1cellbio-v2
inDrops version 3 (16 bp barcode, 6 bp UMI): indrops-v3, 1cellbio-v3
Nadia (12 bp barcode, 8 bp UMI): nadia, dropseq
MARS-Seq (6 bp barcode, 10 bp UMI): marsseq, marsseq-v1
MARS-Seq2 (7 bp barcode, 8 bp UMI): marsseq2, marsseq-v2
Microwell-Seq (18 bp barcode, 6 bp UMI): microwell
PIP-Seq version 0 (24 bp barcode, 8 bp UMI): pip-seq-v0
PIP-Seq version 1 (16 bp barcode, 6 bp UMI): pip-seq-v1
PIP-Seq version 2 (24 bp barcode, 12 bp UMI): pip-seq-v2
PIP-Seq version 3 (28 bp barcode, 12 bp UMI): pip-seq-v3, fluent-bio-v3
PIP-Seq version 4 (28 bp barcode, 12 bp UMI): pip-seq-v4, fluent-bio-v4
QuartzSeq (6 bp index, no UMI): quartz-seq
Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384
Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536
RamDA-Seq (16 bp barcode, no UMI): ramda-seq
SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2
SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3
SCIFI-Seq (27 bp barcode, 8 bp UMI): scifiseq
SCRB-Seq (6 bp barcode, 10 bp UMI): scrbseq, mcscrbseq
SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3
Smart-seq (16 bp barcode, No UMI): smartseq
Smart-seq2 (16 bp barcode, No UMI): smartseq2
Smart-seq2-UMI, Smart-seq3 (16 bp barcode, 8 bp UMI): smartseq3
SPLiT-Seq (8 bp UMI, 24 bp barcode): splitseq
SPLiT-Seq v2.1 (10 bp UMI, 24 bp barcode): splitseq2
STRT-Seq (6 bp barcode, no UMI): strt-seq
STRT-Seq-C1 (8 bp barcode, 5 bp UMI): strt-seq-c1
STRT-Seq-2i (13 bp barcode, 6 bp UMI): strt-seq-2i
SureCell (18 bp barcode, 8 bp UMI): surecell, ddseq, biorad
VASA-plate (6 bp UMI, 6 bp barcode): vasa-plate
VASA-drop (6 bp UMI, 16 bp barcode): vasa-drop
Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
e.g. Custom (16 bp barcode, 10 bp UMI): custom_16_10
-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', 'SC5P-R1', 'SC5P-R2', 'threeprime', or 'fiveprime'
5\′ scRNA-Seq ('SC5P-PE') is available only for 10x Genomics, ICELL8, SmartSeq, and STRT-Seq technologies.
Setting 'SC3Pv1' for 10x version 1 chemistry is recommended.
All other technologies default to 3\′ scRNA-Seq parameters. Only 10x Genomics, ICELL8, and SmartSeq2 allow choosing which to use.
For SmartSeq2 this parameter detemines using full-length sequences or 5\′ ends with internal reads removed.
-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
--non-umi or --read-only Force counting reads by adding or replacing UMI with a mock sequence.
Default for: Quartz-Seq, RamDA-Seq, Smart-Seq, Smart-Seq2, STRT-Seq, ICELL8 3-prime version2
--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=""
bam=""
secondary=""
library=""
introns=""
noexit=""
nopreflight=""
nonUMI=false
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
;;
--non-umi|--read-only)
nonUMI=true
next=false
shift
;;
--setup)
setup=true
next=false
shift
;;
--as-is)
convert=false
next=false
shift
;;
--include-introns)
introns="include-introns"
next=false
shift
;;
--no-bam)
bam="--no-bam"
next=false
shift
;;
--nosecondary)
secondary="--nosecondary"
next=false
shift
;;
--nolibraries)
library="--nolibraries"
next=false
shift
;;
--noexit)
noexit="--noexit"
next=false
shift
;;
--nopreflight)
nopreflight="--nopreflight"
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 -f 1 -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-v1" ]] || [[ "$technology" == "chromium-v1" ]]; then
technology="10x-v1"
elif [[ "$technology" == "10x-v2" ]] || [[ "$technology" == "chromium-v2" ]]; then
technology="10x-v2"
elif [[ "$technology" == "10x-v3" ]] || [[ "$technology" == "chromium-v3" ]]; then
technology="10x-v3"
elif [[ "$technology" == "bd-rhapsody" ]] || [[ "$technology" == "bd" ]] || [[ "$technology" == "rhapsody" ]] || [[ "$technology" == "bdrhapsody" ]]; then
technology="bd-rhapsody"
elif [[ "$technology" == "bd-rhapsody-v2" ]] || [[ "$technology" == "bd-v2" ]] || [[ "$technology" == "rhapsody-v2" ]] || [[ "$technology" == "bdrhapsody-v2" ]] || [[ "$technology" == "bd-rhapsodyv2" ]] || [[ "$technology" == "bdv2" ]] || [[ "$technology" == "rhapsodyv2" ]] || [[ "$technology" == "bdrhapsodyv2" ]] || [[ "$technology" == "bd-rhapsody-2022" ]] || [[ "$technology" == "bd-2022" ]] || [[ "$technology" == "rhapsody-2022" ]] || [[ "$technology" == "bdrhapsody-2022" ]] || [[ "$technology" == "bd-rhapsody2022" ]] || [[ "$technology" == "bd2022" ]] || [[ "$technology" == "rhapsody2022" ]] || [[ "$technology" == "bdrhapsody2022" ]]; then
technology="bd-rhapsody-v2"
elif [[ "$technology" == "aligent" ]] || [[ "$technology" == "bravo" ]] || [[ "$technology" == "aligent-bravo" ]] || [[ "$technology" == "bravo-b" ]] || [[ "$technology" == "aligent-bravo-b" ]]; then
techology="bravo"
nonUMI=false
elif [[ "$technology" == "c1" ]] || [[ "$technology" == "c1-fluidigm" ]] || [[ "$technology" == "fluidigm" ]] || [[ "$technology" == "fluidigm-c1" ]]|| [[ "$technology" == "fluidigmc1" ]] || [[ "$technology" == "c1-rna-seq" ]]|| [[ "$technology" == "c1-mrna-seq" ]] || [[ "$technology" == "c1-rnaseq" ]]|| [[ "$technology" == "c1-scrna" ]]; then
technology="fluidigm-c1"
nonUMI=true
elif [[ "$technology" == "c1-cage" ]] || [[ "$technology" == "c1cage" ]] || [[ "$technology" == "cage-c1" ]] || [[ "$technology" == "cagec1" ]]; then
technology="c1-cage"
nonUMI=true
elif [[ "$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" ]] || [[ "$technology" == "icell8-v3" ]] || [[ "$technology" == "icell8v3" ]]; then
technology="icell8"
#set as "icell8-5-prime" if called by chemistry
if [[ "$chemistry" == "SC5P-"* ]] || [[ "$chemistry" == "fiveprime" ]]; then
technology="icell8-icell8-5-prime"
nonUMI=true
fi
elif [[ "$technology" == "icell8-non-umi" ]] || [[ "$technology" == "icell8-nonumi" ]] || [[ "$technology" == "icell8-v2" ]] || [[ "$technology" == "icell8v2" ]]; then
technology="icell8"
nonUMI=true
elif [[ "$technology" == "icell8-five-prime" ]] || [[ "$technology" == "icell8fiveprime" ]] || [[ "$technology" == "icell8-5p" ]] || [[ "$technology" == "icell85p" ]]; then
technology="icell8-5-prime"
nonUMI=true
if [[ -z ${chemistry} ]] || [[ ${chemistry} == "SC3Pv"* ]]; then
if [[ $verbose ]]; then
echo "setting chemistry for 5' scRNA"
fi
chemistry="SC5P-PE"
fi
elif [[ "$technology" == "icell8-full" ]] || [[ "$technology" == "icell8-fl" ]] || [[ "$technology" == "icell8fl" ]] || [[ "$technology" == "smartseq-icell8" ]] || [[ "$technology" == "smart-seq-icell8" ]] || [[ "$technology" == "icell8-smart-seq" ]] || [[ "$technology" == "icell8smartseq" ]]; then
technology="icell8-full-length"
nonUMI=true
if [[ -z ${chemistry} ]] || [[ ${chemistry} == "SC3Pv"* ]]; then
if [[ $verbose ]]; then
echo "setting chemistry for 5' scRNA"
fi
chemistry="SC5P-PE"
fi
elif [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrops-v1" ]] || [[ "$technology" == "indropv1" ]] || [[ "$technology" == "indropsv1" ]] || [[ "$technology" == "indrop1" ]] || [[ "$technology" == "indrops1" ]] || [[ "$technology" == "1cellbio-v1" ]] || [[ "$technology" == "1cellbiov1" ]]; then
technology="indrop-v1"
elif [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrops-v2" ]] || [[ "$technology" == "indropv2" ]] || [[ "$technology" == "indropsv2" ]] || [[ "$technology" == "indrop2" ]] || [[ "$technology" == "indrops2" ]] ||[[ "$technology" == "1cellbio-v2" ]] || [[ "$technology" == "1cellbiov2" ]]; then
technology="indrop-v2"
elif [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "indrops-v3" ]] || [[ "$technology" == "indropv3" ]] || [[ "$technology" == "indropsv3" ]] || [[ "$technology" == "indrop3" ]] || [[ "$technology" == "indrops3" ]] || [[ "$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" == "microwell-seq" ]] || [[ "$technology" == "micro-well" ]] || [[ "$technology" == "microwell" ]] || [[ "$technology" == "microwellseq" ]]; then
technology="microwellseq"
elif [[ "$technology" == "pip-seq-v0" ]] || [[ "$technology" == "pip-seq-V0" ]] || [[ "$technology" == "pipseq-v0" ]] || [[ "$technology" == "pip-seqv0" ]] || [[ "$technology" == "pipseqv0" ]] || [[ "$technology" == "delley" ]] || [[ "$technology" == "delley2021" ]] || [[ "$technology" == "delley-2021" ]]; then
technology="pip-seq-v0"
elif [[ "$technology" == "pip-seq" ]] || [[ "$technology" == "pip-seq-v1" ]] || [[ "$technology" == "pip-seq" ]] || [[ "$technology" == "pip-seq-v1" ]] || [[ "$technology" == "pipseq" ]] || [[ "$technology" == "pipseq-v1" ]] || [[ "$technology" == "pip-seqv1" ]] || [[ "$technology" == "pipseqv1" ]]; then
technology="pip-seq-v1"
elif [[ "$technology" == "pip-seq-v2" ]] || [[ "$technology" == "pip-seq-V2" ]] || [[ "$technology" == "pipseq-v2" ]] || [[ "$technology" == "pip-seqv2" ]] || [[ "$technology" == "pipseqv2" ]]; then
technology="pip-seq-v2"
elif [[ "$technology" == "pip-seq-v3" ]] || [[ "$technology" == "pip-seq-V3" ]] || [[ "$technology" == "pipseq-v3" ]] || [[ "$technology" == "pip-seqv3" ]] || [[ "$technology" == "pipseqv3" ]] || [[ "$technology" == "fluent-bio-v3" ]] || [[ "$technology" == "fluentbio-v3" ]] || [[ "$technology" == "fluent-biov3" ]] || [[ "$technology" == "fluentbiov3" ]]; then
technology="pip-seq-v3"
elif [[ "$technology" == "pip-seq-v4" ]] || [[ "$technology" == "pip-seq-V4" ]] || [[ "$technology" == "pipseq-v4" ]] || [[ "$technology" == "pip-seqv4" ]] || [[ "$technology" == "pipseqv4" ]] || [[ "$technology" == "fluent-bio-v4" ]] || [[ "$technology" == "fluentbio-v4" ]] || [[ "$technology" == "fluent-biov4" ]] || [[ "$technology" == "fluentbiov4" ]]; then
technology="pip-seq-v4"
elif [[ "$technology" == "quartz-seq" ]] || [[ "$technology" == "quartzseq" ]] || [[ "$technology" == "quartz-seq1" ]]; then
technology="quartz-seq"
nonUMI=true
elif [[ "$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" == "rambda-seq" ]] || [[ "$technology" == "lamda-seq" ]] || [[ "$technology" == "lambda-seq" ]] || [[ "$technology" == "ramdaseq" ]] || [[ "$technology" == "ram-da-seq" ]] || [[ "$technology" == "ramda-seq" ]]; then
technology="ramda-seq"
nonUMI=true
elif [[ "$technology" == "rambda-seq-c1" ]] || [[ "$technology" == "lamda-seq-c1" ]] || [[ "$technology" == "lambda-seq-c1" ]] || [[ "$technology" == "ramdaseqc1" ]] || [[ "$technology" == "ram-da-seq-c1" ]] || [[ "$technology" == "ramda-seq-c1" ]] || [[ "$technology" == "ramda-seqc1" ]] || [[ "$technology" == "c1-rambda-seq" ]] || [[ "$technology" == "c1-lamda-seq" ]] || [[ "$technology" == "c1-lambda-seq" ]] || [[ "$technology" == "c1-ramdaseq" ]] || [[ "$technology" == "c1-ram-da-seq" ]] || [[ "$technology" == "c1ramda-seq" ]] || [[ "$technology" == "c1-ramda-seq" ]]; then
technology="c1-ramda-seq"
nonUMI=true
elif [[ "$technology" == "sciseq" ]] || [[ "$technology" == "sci-seq" ]] || [[ "$technology" == "sci-rna-seq" ]]; then
technology="sciseq3"
elif [[ "$technology" == "sciseq2" ]] || [[ "$technology" == "sci-seq2" ]]; then
technology="sciseq2"
elif [[ "$technology" == "sciseq3" ]] || [[ "$technology" == "sci-seq3" ]] || [[ "$technology" == "sci-rna-seq3" ]] || [[ "$technology" == "sci-rna-seq-3" ]] ; then
technology="sciseq3"
elif [[ "$technology" == "scifiseq" ]] || [[ "$technology" == "scifi-seq" ]] || [[ "$technology" == "sci-fi-seq" ]] || [[ "$technology" == "scifi-rna-seq" ]]; then
technology="scifiseq"
elif [[ "$technology" == "scrbseq" ]] || [[ "$technology" == "scrb-seq" ]] || [[ "$technology" == "mcscrbseq" ]] || [[ "$technology" == "mcscrb-seq" ]]; then
technology="scrbseq"
elif [[ "$technology" == "plexwell" ]] || [[ "$technology" == "plex-well" ]] || [[ "$technology" == "seqwell" ]] || [[ "$technology" == "seq-well" ]] || [[ "$technology" == "seqwells3" ]] || [[ "$technology" == "seq-well-s3" ]]; 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 [[ "$technology" == "splitseq2" ]] || [[ "$technology" == "split-seq2" ]] || [[ "$technology" == "splitseq-v2" ]] || [[ "$technology" == "split-seq-v2" ]] || [[ "$technology" == "parse" ]] || [[ "$technology" == "parsebio" ]] || [[ "$technology" == "parse-bio" ]] || [[ "$technology" == "evercode" ]]; then
technology="splitseq2"
elif [[ "$technology" == "strt-seq" ]] || [[ "$technology" == "strt" ]] || [[ "$technology" == "strtseq" ]]; then
technology="strt-seq"
nonUMI=true
if [[ -z ${chemistry} ]] || [[ ${chemistry} == "SC3Pv"* ]]; then
if [[ $verbose ]]; then
echo "setting chemistry for 5\' scRNA"
fi
chemistry="SC5P-R1"
fi
elif [[ "$technology" == "strt-seq-c1" ]] || [[ "$technology" == "strt-seqc1" ]] || [[ "$technology" == "strtseqc1" ]] || [[ "$technology" == "strtseq-c1" ]]; then
technology="strt-seq-c1"
elif [[ "$technology" == "strt-seq-2i" ]] || [[ "$technology" == "strt-seq2i" ]] || [[ "$technology" == "strtseq2i" ]] || [[ "$technology" == "strtseq-2i" ]]; then
technology="strt-seq-2i"
elif [[ "$technology" == "strt-seq-2018" ]] || [[ "$technology" == "strt-seqc2018" ]] || [[ "$technology" == "strtseq2018" ]] || [[ "$technology" == "strtseq-2018" ]] || [[ "$technology" == "strt-seq-v3" ]]; then
technology="strt-seq-2018"
if [[ -z ${chemistry} ]] || [[ ${chemistry} == "SC5P"* ]]; then
if [[ $verbose ]]; then
echo "setting chemistry for 3\' scRNA PE"
fi
chemistry="SC3Pv2"
fi
elif [[ "$technology" == "surecell" ]] || [[ "$technology" == "surecellseq" ]] || [[ "$technology" == "surecell-seq" ]] || [[ "$technology" == "ddseq" ]] || [[ "$technology" == "dd-seq" ]] || [[ "$technology" == "bioraad" ]]; then
technology="surecell"
elif [[ "$technology" == "vasa-seq-plate" ]] || [[ "$technology" == "vasa-seq" ]] || [[ "$technology" == "vasa-plate" ]] || [[ "$technology" == "vasaplate" ]] || [[ "$technology" == "vasa" ]]; then
technology="vasa-plate"
elif [[ "$technology" == "vasa-seq-drop" ]] || [[ "$technology" == "vasa-drop-seq" ]] || [[ "$technology" == "vasa-drop" ]] || [[ "$technology" == "vasadrop" ]] || [[ "$technology" == "vasa-droplet" ]]; then
technology="vasa-drop"
elif [[ "$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 -f 2 -d'_'`
u=`echo $technology | cut -f 3 -d'_'`
if ! [[ "$b" =~ ^[0-9]+$ ]] || ! [[ "$u" =~ ^[0-9]+$ ]]; then
echo "Error: option -t needs to be a technology listed or custom_<barcode>_<UMI>"
exit 1
fi
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: ${technology}-v3 should only be used for kits that have valid UMIs***"
fi
if [[ "$technology" == "smartseq2-umi" ]] || [[ "$technology" == "smartseq3" ]]; then
echo "***WARNING: ${technology} should only be used for kits that have UMIs***"
echo "... UMI reads will be filtered using a tag sequence which will be subsequently removed"
echo "... barcodes will be derived from dual indexes"
fi
if [[ "$technology" == "smartseq2" ]] || [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrop-v3" ]]; then
echo "***Note: 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 [[ "$technology" == "10x-v1" ]]; then
barcodelength=14
barcode_default=14
umilength=10
minlength=14
chemistry="SC3Pv1"
technology="10x"
elif [[ "$technology" == "10x-v2" ]]; then
barcodelength=16
umilength=10
minlength=16
technology="10x"
elif [[ "$technology" == "10x-v3" ]]; then
barcodelength=16
umilength=12
minlength=16
chemistry="SC3Pv3"
technology="10x"
elif [[ "$technology" == "bd-rhapsody" ]] || [[ "$technology" == "bd-rhapsody-v2" ]]; then
barcodelength=27
umilength=8
minlength=27
elif [[ "$technology" == "fluidigm-c1" ]]; then
barcodelength=16
umilength=0
minlength=16
elif [[ "$technology" == "c1-cage" ]]; then
barcodelength=16
umilength=0
minlength=16
elif [[ "$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
if [[ $nonUMI == "true" ]]; then
umilength=0
else
umilength=14
fi
minlength=11
elif [[ "$technology" == "icell8-5-prime" ]]; then
barcodelength=10
if [[ $nonUMI == "true" ]]; then
umilength=0
else
umilength=8
fi
minlength=10
elif [[ "$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" == "microwellseq" ]]; then
barcodelength=18
umilength=6
minlength=18
elif [[ "$technology" == "marsseq-v2" ]]; then
barcodelength=7
umilength=8
minlength=7
elif [[ "$technology" == "pip-seq-v0" ]]; then
barcodelength=27
umilength=8
minlength=24
elif [[ "$technology" == "pip-seq-v1" ]]; then
barcodelength=19
umilength=6
minlength=16
elif [[ "$technology" == "pip-seq-v2" ]]; then
barcodelength=24
umilength=12
minlength=24
elif [[ "$technology" == "pip-seq-v3" ]]; then
barcodelength=28
umilength=12
minlength=28
elif [[ "$technology" == "pip-seq-v4" ]]; then
barcodelength=31
umilength=12
minlength=28
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 [[ "$technology" == "sciseq2" ]]; then
barcodelength=30
umilength=8
minlength=30
elif [[ "$technology" == "sciseq3" ]]; then
barcodelength=40
umilength=8
minlength=40