Commit a9d984ad authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

Merge branch 'kai' of dgt-gitlab.gsc.riken.jp:tom/cellranger_convert

parents 74e9b127 0ab06d24

launch_universc.sh

+143 −165
Original line number Diff line number Diff line
@@ -8,7 +8,7 @@ if [[ -z $cellrangerpass ]]; then 
    echo "cellranger command is not found."

    exit 1

fi

ver_info=`paste -d "\n" <(cellranger count --version) <(echo conversion script version 0.2.0.9002) | head -n 3 | tail -n 2`

ver_info=`paste -d "\n" <(cellranger count --version) <(echo conversion script version 0.2.0.900333) | head -n 3 | tail -n 2`

##########
@@ -39,28 +39,28 @@ echo "Running launch_universc.sh in '$SCRIPT_DIR'" 
#####usage statement#####

help='

Usage:

  bash $(basename "$0") -R1 FILE1 -R2 FILE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  bash $(basename "$0") -R1 READ1_LANE1 READ1_LANE2 -R2 READ2_LANE1 READ2_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option=OPT]

  bash $(basename "$0") -f SAMPLE_LANE -t TECHNOLOGY -i ID -r REFERENCE [--option=OPT]

  bash $(basename "$0") -f \"SAMPLE_LANE1 SAMPLE_LANE2\" -t TECHNOLOGY -i ID -r REFERENCE [--option=OPT]

  bash $(basename "$0") -v

  bash $(basename "$0") -h

  bash $(basename "$0") -t TECHNOLOGY --setup

  bash '$(basename $0)' -R1 FILE1 -R2 FILE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  bash '$(basename $0)' -R1 READ1_LANE1 READ1_LANE2 -R2 READ2_LANE1 READ2_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  bash '$(basename $0)' -f SAMPLE_LANE -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  bash '$(basename $0)' -f SAMPLE_LANE1 SAMPLE_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]

  bash '$(basename $0)' -v

  bash '$(basename $0)' -h

  bash '$(basename $0)' -t TECHNOLOGY --setup



Convert sequencing data (FASTQ) from various platforms for compatibility with 10x Genomics and run cellranger count



Mandatory arguments to long options are mandatory for short options too.

  -s,  --setup                  Set up whitelists for compatibility with new technology

  -t,  --technology=PLATFORM    Name of technology used to generate data (10x, nadia, icell8)

  -R1, --read1=FILE             Read 1 FASTQ file to pass to cellranger (cell barcodes and umi)

  -R2, --read2=FILE             Read 2 FASTQ file to pass to cellranger

  -f,  --file=NAME              Name of FASTQ files to pass to cellranger (prefix before R1 or R2)

  -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.

  -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

  -t,  --technology PLATFORM    Name of technology used to generate data (10x, nadia, icell8)

  -R1, --read1 FILE             Read 1 FASTQ file to pass to cellranger (cell barcodes and umi)

  -R2, --read2 FILE             Read 2 FASTQ file to pass to cellranger

  -f,  --file NAME              Name of FASTQ files to pass to cellranger (prefix before R1 or R2)

  -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.

  -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

  -w,  --overwrite              How to carry out FASTQ file conversions: 'skip' to skip conversion, 'convert' to overwrite all preexisting converted files, and 'keep' (default) to only convert files that do not already exist.

  -h,  --help                   Display this help and exit

  -v,  --version                Output version information and exit
@@ -82,8 +82,18 @@ fi 






#####reading in options#####

setup="false"

#####options#####

#set options

DIR=`which cellranger` #location of cellranger

VERSION=`cellranger count --version | head -n 2 | tail -n 1 | cut -d"(" -f2 | cut -d")" -f1` #get cellranger version

lockfile=${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock #path for .lock file

lastcallfile=${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called #path for .last_called

lastcall=`cat $lastcallfile`

barcodefolder=${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes #folder with the barcodes

cdrIN="input4cellranger" #name of the directory with all FASTQ files given to cellranger



#variable options

setup=false

read1=()

read2=()

SAMPLE=""
@@ -94,10 +104,7 @@ reference="" 
ncells=""

chemistry=""

jobmode=""

convert="keep"



DIR=`which cellranger`

VERSION=`cellranger count --version | head -n 2 | tail -n 1 | cut -d"(" -f2 | cut -d")" -f1`

convert=keep



next=false

for op in "$@"; do
@@ -123,6 +130,7 @@ for op in "$@"; do 
        shift

            if [[ $1 != "" ]]; then

                technology="${1/%\//}"

                technology=`echo "$technology" | tr '[:upper:]' '[:lower:]'`

                next=true

                shift

            else
@@ -162,8 +170,7 @@ for op in "$@"; do 
            ;;

        -f|--file)

            shift

            if [[ "$1" != "" ]]

                then

            if [[ "$1" != "" ]]; then

                arg=$1

                while [[ ! "$arg" == "-"* ]] && [[ "$arg" != "" ]]; do

                    read1+=("${1}_R1_001")
@@ -268,53 +275,7 @@ for op in "$@"; do 
done

##########



#####check if UniverSC is running already#####

#create .lock file if none exists

if [[ ! -f  ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock ]]; then

    echo "creating lock file"

    echo 0 > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

fi



#check if jobs running (check value in .lock file)

echo "checking .lock file"

lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`



if [[ ! $lock == "0" ]]; then

    echo " $lock number of cellranger ${VERSION} jobs already running in ${DIR}"

    #check technology current running

    if [[ -f ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called ]]; then

        last=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called`

        echo " running $lock jobs with technology $last"

        #check if the technology running is different from the current convert call

        if [[ $last == $technology ]]; then

            echo " no conflict detected"

            #add disable increment for setup calls (which are not counted or removed)

            if [[ $setup == false ]]; then

                #add current job to lock

                echo " increment lock"

                lock=$(($lock+1))

                echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

                echo " call accepted: running $lock cellranger jobs on $technology"

            fi

	else

	    echo "Error: conflict between technology selected for the new job ($technology) and for $lock jobs currently running ($last)"

            echo "barcode whitelist configured and locked for currently running technology: $last"

            echo "remove ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock if $last jobs have completed or aborted"

            exit 1

        fi

    fi

else

    #initialise lock file if first call (no other jobs running)

    #add disable increment for setup calls (which are not counted or removed)

    if [[ $setup == false ]]; then

        #add current job to lock

        echo " increment lock"

        lock=$(($lock+1))

        echo " call accepted: running no other cellranger jobs"

        echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

    fi

fi

##########



#####check if input maches expected inputs#####

if [[ $verbose == "true" ]]; then
@@ -322,26 +283,21 @@ if [[ $verbose == "true" ]]; then 
fi



#check if technology matches expected inputs

technology=`echo "$technology" | tr '[:upper:]' '[:lower:]'`

if [[ "$technology" != "10x" ]] && [[ "$technology" != "nadia" ]] && [[ "$technology" != "icell8" ]]; then

    echo "Error: option -t needs to be 10x, nadia, or icell8"

    exit 1

fi



#check if setup needs to be run before analysis

if [[ -z $setup ]]; then

    setup=false

fi



#check for presence of read1 and read2 files

if [[ ${#read1[@]} -eq 0 ]] && [[ $setup == "false" ]]; then

if [[ $setup == "false" ]]; then

    if [[ ${#read1[@]} -eq 0 ]]; then

        echo "Error: option -R1 or --file is required"

        exit 1

fi

if [[ ${#read2[@]} -eq 0 ]] && [[ $setup == "false" ]]; then

    elif [[ ${#read2[@]} -eq 0 ]]; then

        echo "Error: option -R2 or --file is required"

        exit 1

    fi

fi



#check for file type (extension) for files

##allows incomplete file names and processing compressed files
@@ -357,9 +313,11 @@ for i in ${!read1[@]}; do 
            read=`echo $read | sed -e "s/\.gz//g"`

        fi

        if [[ $read != *"fastq" ]] && [[ $read != *"fq" ]]; then

            echo "***Warning: file $read is assubed to be in fastq format***"

            echo "***Warning: file $read is assumed to be in fastq format***"

        fi

        if [[ $verbose == "true" ]]; then

            echo "  $read"

        fi

    elif [[ -f $read ]]; then

        if [[ $read == *"gz" ]]; then

            gunzip -k $read
@@ -369,7 +327,9 @@ for i in ${!read1[@]}; do 
        if [[ $read != *"fastq" ]] && [[ $read != *"fq" ]]; then

            echo "***Warning: file $read is assubed to be in fastq format***"

        fi

        if [[ $verbose == "true" ]]; then

            echo "  $read"

        fi

    else

        echo "Error: $read not found"

        exit 1
@@ -391,7 +351,9 @@ for i in ${!read2[@]}; do 
        if [[ $read != *"fastq" ]] && [[ $read != *"fq" ]]; then

            echo "***Warning: file $read is assubed to be in fastq format***"

        fi

        if [[ $verbose == "true" ]]; then

	    echo "  $read"

	fi

    elif [[ -f $read ]]; then

        if [[ $read == *"gz" ]]; then

            gunzip -k $read
@@ -401,7 +363,9 @@ for i in ${!read2[@]}; do 
        if [[ $read != *"fastq" ]] && [[ $read != *"fq" ]]; then

            echo "***Warning: file $read is assubed to be in fastq format***"

        fi

        if [[ $verbose = "true" ]]; then

            echo "  $read"

        fi

    else

        echo "Error: $read not found"

        exit 1
@@ -413,6 +377,7 @@ done 
if [[ $verbose == "true" ]]; then

    echo " checking file name for $read1 ..."

fi



for i in ${!read1[@]}; do

    read=${read1[$i]}

    if [[ -h $read ]]; then
@@ -607,7 +572,7 @@ done 
LANE=$(echo "${LANE[@]}" | tr ' ' '\n' | sort -u | tr '\n' ',' | sed 's/,$//')



#check if ID is present

if [[ -z $id ]] && ! [[ ${#read1[@]} -eq 0 ]]; then

if [[ -z $id ]] && [[ ${#read1[@]} -eq 0 ]]; then

    echo "Error: option --id is required"

    exit 1

elif [[ $id == *" "* ]]; then
@@ -616,10 +581,12 @@ elif [[ $id == *" "* ]]; then 
fi



#check if reference is present

if [[ -z $reference ]] && [[ $setup == "false" ]]; then

    echo "Error: option --reference is required"

if [[ -z $reference ]]; then

    if [[ $setup == "false" ]] || [[ ${#read1[@]} -ne 0 ]] || [[ ${#read2[@]} -ne 0 ]]; then

        echo "Error: option --reference is required";

        exit 1

    fi

fi



#check if ncells is an integer

int='^[0-9]+$'
@@ -651,6 +618,53 @@ if [[ "$convert" != "keep" ]] && [[ "$convert" != "skip" ]] && [[ "$convert" != 
    echo "Error: option --overwrite needs to be keep, skip, or convert"

    exit 1

fi



#check if setup needs to be run before analysis

if [[ -z $setup ]]; then

    setup=false

fi

if [[ $lastcall != $technology ]]; then

    setup=true

fi

##########







#####check if UniverSC is running already#####

#set up .lock file

if [[ ! -f $lockfile ]]; then

    echo "creating .lock file"

    echo 0 > $lockfile

else

    #check if jobs running (check value in .lock file)

    echo "checking .lock file"

    lock=`cat $lockfile`

    

    if [[ $lock -eq 0 ]]; then

        echo " call accepted: no other cellranger jobs running"

        lock=1

        echo $lock > $lockfile

    else

        if [[ -f $lastcallfile ]]; then

            echo " total of $lock cellranger ${VERSION} jobs already running in ${DIR} with technology $lastcall"

            

            #check if the technology running is different from the current convert call

            if [[ $lastcall == $technology ]]; then

                echo " call accepted: no conflict detected with other jobs currently running"

                #add current job to lock

                lock=$(($lock+1))

                echo $lock > $lockfile

	    else

	        echo "Error: conflict between technology selected for the new job ($technology) and other jobs currently running ($lastcall)"

                echo "barcode whitelist configured and locked for currently running technology: $lastcall"

                echo "remove $lockfile if $lastcall jobs have completed or aborted"

                exit 1

            fi

        else

            echo "Error: $lastcallfile not found"

        fi

    fi

fi

##########
@@ -659,17 +673,13 @@ fi 
echo ""

echo "#####Input information#####"

echo "SETUP: $setup"

if ! [[ $setup == "false" ]]; then

    echo "***Warning: whitelist is converted for compatibility, valid barcodes cannot be detected accurately with this technology***"

echo "FORMAT: $technology"

if [[ $technology == "nadia" ]]; then

    echo "***Warning: whitelist is converted for compatibility with $technology, valid barcodes cannot be detected accurately with this technology***"

fi

if [[ ${#read1[@]} -eq 0 ]] && [[ ${#read1[@]} -eq 0 ]]; then

    echo "***Warning: no FASTQ files were selected, launch_universc.sh will exit after setting up the whitelist***"

fi

fi

if ! [[ "$technology" == "10x" ]]; then

    echo "FORMAT: $technology"

else

    echo "FORMAT: $technology (no conversion)"

fi

if ! [[ ${#read1[@]} -eq 0 ]]; then

    echo "INPUT(R1):"

    for i in ${!read1[@]}; do
@@ -714,7 +724,7 @@ echo "" 
#run setup if called

if [[ $setup == "true" ]]; then

    echo "setup begin"

    if [[ ! -w ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes ]]; then

    if [[ ! -w $barcodefolder ]]; then

        echo "Error: launch_universc.sh can only be run cellranger installed locally"

        echo "Running cellranger installed at $DIR"

        echo "Install cellranger in a directory with write permissions such as /home/`whoami`/local"
@@ -723,13 +733,14 @@ if [[ $setup == "true" ]]; then 
        echo " `whereis cellranger`"

        exit 1

    fi

    cd ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes

    

    cd $barcodefolder

    

    if [[ -f 3M-february-2018.txt ]]; then

        gzip -f 3M-february-2018.txt

    fi

    

    echo "updating barcodes in ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes for cellranger version $VERSION installed in $DIR ..."

    echo "updating barcodes in $barcodefolder for cellranger version $VERSION installed in $DIR ..."

    

    if [[ $technology == "10x" ]]; then

        #restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8)
@@ -752,8 +763,7 @@ if [[ $setup == "true" ]]; then 
        #if cellranger version is 3 or greater, restore assert functions

        if [[ `printf '%s\n' '$VERSION 3.0.0' | sort -V | head -n 1` != $VERSION ]]; then

            #restore functions if other technology run previously

            last=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called`

            if [[ $last != $technology ]]; then

            if [[ $lastcall != $technology ]]; then

                sed -i "s/#assert barcode_idx >= prev_barcode_idx/assert barcode_idx >= prev_barcode_idx/g" ${DIR}-cs/${VERSION}/mro/stages/counter/report_molecules/__init__.py

                sed -i "s/#assert np.array_equal(in_mc.get_barcodes(), barcodes)/assert np.array_equal(in_mc.get_barcodes(), barcodes)/g" ${DIR}-cs/${VERSION}/lib/python/cellranger/molecule_counter.py

            fi
@@ -782,7 +792,6 @@ if [[ $setup == "true" ]]; then 
            echo " backing up whitelist of version 2 kit ..."

            cp 737K-august-2016.txt 737K-august-2016.txt.backup

        fi

        echo "Warning: Valid barcodes cannot be calculated accurately for Nadia or DropSeq technology"

        #combine 10x and Nadia barcodes

        cat nadia_barcode.txt 737K-august-2016.txt.backup | sort | uniq > 737K-august-2016.txt

        echo " whitelist converted for Nadia compatibility with version 2 kit."
@@ -814,8 +823,7 @@ if [[ $setup == "true" ]]; then 
        #if cellranger version is 3 or greater, restore assert functions

        if [[ `printf '%s\n' '$VERSION 3.0.0' | sort -V | head -n 1` != $VERSION ]]; then

            #disable functions if 10x technology run previously

            last=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called`

            if [[ $last != "10x" ]]; then

            if [[ $lastcall != "10x" ]]; then

                sed -i "s/assert barcode_idx >= prev_barcode_idx/#assert barcode_idx >= prev_barcode_idx/g" ${DIR}-cs/${VERSION}/mro/stages/counter/report_molecules/__init__.py

                sed -i "s/assert np.array_equal(in_mc.get_barcodes(), barcodes)/#assert np.array_equal(in_mc.get_barcodes(), barcodes)/g"  ${DIR}-cs/${VERSION}/lib/python/cellranger/molecule_counter.py

            fi
@@ -880,8 +888,7 @@ if [[ $setup == "true" ]]; then 
        #if cellranger version is 3 or greater, restore assert functions

        if [[ `printf '%s\n' '$VERSION 3.0.0' | sort -V | head -n 1` != $VERSION ]]; then

            #disable functions if 10x technology run previously

            last=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called`

            if [[ $last != "10x" ]]; then

            if [[ $lastcall != "10x" ]]; then

                sed -i "s/assert barcode_idx >= prev_barcode_idx/#assert barcode_idx >= prev_barcode_idx/g" ${DIR}-cs/${VERSION}/mro/stages/counter/report_molecules/__init__.py

                sed -i "s/assert np.array_equal(in_mc.get_barcodes(), barcodes)/#assert np.array_equal(in_mc.get_barcodes(), barcodes)/g" ${DIR}-cs/${VERSION}/lib/python/cellranger/molecule_counter.py

            fi
@@ -890,16 +897,22 @@ if [[ $setup == "true" ]]; then 
            echo "$DIR ready for $technology"

        fi

    else

        lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

        lock=$(($lock-1))

        echo $lock > $lockfile

        echo "Error: technology ($technology) is not supported"

        cd -

        exit 1

    fi

    echo $technology > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called

    echo $technology > $lastcallfile

    cd -

    echo "setup complete"

fi



if [[ ${#read1[@]} -eq 0 ]] && [[ ${#read2[@]} -eq 0 ]]; then

    lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

    lock=$(($lock-1))

    echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

    echo " whitelist converted and no FASTQ files are selected. exiting launch_universc.sh"

    exit 0

fi
@@ -907,37 +920,8 @@ fi 






#####detect whitelist directory#####

#check whitelist and run --setup if needed

echo "checking whitelist ..."

if [[ -f ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called ]]; then

    #run again if last technology called is different from technology

    last=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called`

    if [[ $last != $technology ]]; then

        echo " running setup on $technology on whitelist in ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes ..."

        if [[ $verbose == "true" ]]; then

            echo " last: $last"

            echo " technology: $technology"

        fi

        bash $(basename "$0") -t $technology --setup

        setup=false

        if [[ $convert == "skip" ]]; then

            echo " ***Warning: technology changed to $technology since last run. FASTQ file conversion will be carreid out.***"

            convert="convert"

        fi

    fi

else    

    echo " using setup $technology from previous whitelist configuration ..."

    echo $technology > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called

fi

echo "check complete"

##########







#####create directory with files fed to cellranger#####

echo "creating a folder for all cellranger input files ..."

crIN="cellranger"

convFiles=()



if [[ ! -d $crIN ]]; then
@@ -1032,6 +1016,8 @@ fi 


#####run cellranger#####

echo "running cellranger ..."

echo ""

echo "#####cellranger#####"

d=""

if [[ -n $description ]]; then

    d="--description=$description"
@@ -1071,6 +1057,8 @@ cellranger count --id=$id \ 
#        --nopreflight

end=`date +%s`

runtime=$((end-start))

echo "##########"

echo ""

##########
@@ -1078,26 +1066,17 @@ runtime=$((end-start)) 
#####remove files if convert is not running elsewhere#####

echo "updating .lock file"



#reset lock counter (read in case changed by other jobs)

lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`



#remove currewnt job from counter (successfully completed)

lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

lock=$(($lock-1))



#check if jobs running

if [[ $lock -ge 1 ]]; then

    echo "$lock number of cellranger ${VERSION} jobs still running in ${DIR}"

    #check technology current running

    if [[ -f ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called ]]; then

        last=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called`

        echo "running technology $last with $lock jobs"

    fi

fi



#remove .lock file if no other jobs running exists (prevents negative values allowing technologies to run at same time)

if [[ $lock -le 0 ]]; then

    echo "no other jobs currently running: lock files cleared for cellranger ${VERSION} in ${DIR}"

    echo " total of $lock jobs for $lastcall technology are still run by cellranger ${VERSION} in ${DIR}"

else

    echo " no other jobs currently run by cellranger ${VERSION} in ${DIR}"

    echo " no conflicts: whitelist can now be changed for other technologies"

    rm -f ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

    rm -f $lockfile

fi

##########
@@ -1117,4 +1096,3 @@ echo "$log" 
##########



exit 0

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