Commit 8fa4c886 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

Merge branch 'master' of github.com:TomKellyGenetics/cellranger_convert

parents f6c44589 af4d68e3

.gitattributes

+25 −0
Original line number Diff line number Diff line
@@ -4,3 +4,28 @@ test/cellranger_reference/cellranger-tiny-ref/1.2.0/genes filter=lfs diff=lfs me 
test/cellranger_reference/cellranger-tiny-ref/1.2.0/pickle filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/1.2.0/reference.json filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/1.2.0/star filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0 filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/genes filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/pickle filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/reference.json filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/exonGeTrInfo.tab filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/genomeParameters.txt filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/sjdbList.fromGTF.out.tab filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta/genome.fa filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta/genome.fa.fai filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/pickle/genes.pickle filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/chrNameLength.txt filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/Genome filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/chrLength.txt filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/exonInfo.tab filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/geneInfo.tab filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/sjdbInfo.txt filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/sjdbList.out.tab filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/transcriptInfo.tab filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/genes/genes.gtf filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SAindex filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/chrName.txt filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/chrStart.txt filter=lfs diff=lfs merge=lfs -text

launch_universc.sh

+40 −12
Original line number Diff line number Diff line
@@ -69,9 +69,9 @@ Mandatory arguments to long options are mandatory for short options too. 
  -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 (10x, nadia, icell8, or custom)

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

                                e.g. custom_16_10

  -b,  --barcodefile FILE       Custom barcode list in plain text  

  -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.
@@ -138,7 +138,13 @@ id="" 
description=""

reference=""

ncells=""

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

    #set default chemistry to auto detect 10x version 2 or 3

    chemistry="auto"

else

    #otherwise use version 2 configurations for other platforms

    chemistry="SC3Pv2"

fi

jobmode="local"

ncores=""

mem=""
@@ -418,6 +424,17 @@ if ! [[ -w "$SDIR" ]]; then 
    exit 1

fi





#aliases for technology with the same settings

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

    echo "Running with technology 10x (chromium)" 

    technology="10x"

fi

if [[ "$technology" == "dropseq" ]] || [[ "$technology" == "drop-seq" ]]; then

    echo "Running with Nadia parameters (Drop-Seq)"

    technology="nadia"

fi



#check if technology matches expected inputs

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

    if [[ "$technology" != "custom"* ]]; then
@@ -645,10 +662,12 @@ if [[ ! -z "$barcodefile" ]]; then 
	exit 1

    else

        barcodefile=`readlink -f $barcodefile`

        #all barcodes upper case

        sed -i 's/.*/\U&/g' $barcodefile

    fi

else

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

        barcodefile=default

        barcodefile="default"

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

        barcodefile=${SDIR}/nadia_barcode.txt

        if [[ ! -f ${barcodefile} ]]; then
@@ -696,8 +715,8 @@ elif ! [[ $mem =~ $int ]] && [[ $setup == "false" ]]; then 
fi



#check if chemistry matches expected input

if [[ "$chemistry" != "SC3Pv2" ]] && [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then

    echo "Error: option --chemistry must be SC3Pv2, SC5P-PE , or SC5P-R2"

if [[ "$chemistry" != "SC3Pv3" ]] && [[ "$chemistry" != "SC3Pv2" ]] && [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then

    echo "Error: option --chemistry must be SC3Pv3, SC3Pv2, SC5P-PE , or SC5P-R2"

    exit 1

fi
@@ -758,7 +777,7 @@ umiadjust=`echo $(($umilength-$umi_default))` 
#set up .lock file

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

    echo "creating .lock file"

    echo 1 > $lockfile

    echo 0 > $lockfile

    lock=`cat $lockfile`

else

    #check if jobs are running (check value in .lock file)
@@ -768,22 +787,28 @@ else 
    if [[ $lock -le 0 ]]; then

        echo " call accepted: no other cellranger jobs running"

        lock=1

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

                    echo $lock > $lockfile

        fi

    else

        if [[ -f $lastcallfile ]]; then

	    echo " total of $lock cellranger ${cellrangerversion} jobs are already running in ${cellrangerpath} with barcode length (${lastcall_b}), UMI length (${lastcall_u}), and whitelist barcodes (${lastcall_p})"

            

	    #check if a custom barcode is used for a run (which cannot be run in parallel)

            if [[ ${barcode_length} == ${lastcall_b} ]] && [[ ${umilength} == ${lastcall_u} ]] && [[ ${barcodefile} == ${lastcall_p} ]]; then

            if [[ ${barcodelength} == ${lastcall_b} ]] && [[ ${umilength} == ${lastcall_u} ]] && [[ ${barcodefile} == ${lastcall_p} ]]; then

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

                #add current job to lock

                lock=$(($lock+1))

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

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

                    echo $lock > $lockfile

                fi

            else

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

                echo "make sure that the barcode length, UMI length, and the whitelist barcodes are the same as the other jobs currently running"

                echo "if confident that no other jobs are running and still get this error, remove $lockfile and try again"

                if [[ $verbose ]]; then

                    echo "Submitted configuration with barcode length (${barcodelength}), UMI length (${umilength}), and whitelist barcodes (${barcodefile})"

                fi

                exit 1

            fi

        else
@@ -854,7 +879,7 @@ echo "" 




####setup whitelist#####

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

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

    echo "setup begin"

    echo "updating barcodes in $barcodedir for cellranger version ${cellrangerversion} installed in ${cellrangerpath} ..."
@@ -917,8 +942,10 @@ if [[ $lock -eq 1 ]]; then 
    cd - > /dev/null

    

    echo "setup complete"

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

        exit 0

    fi

fi

#########
@@ -1114,9 +1141,10 @@ echo "cellranger run complete" 
#####remove files if convert is not running elsewhere#####

echo "updating .lock file"



#remove currewnt job from counter (successfully completed)

#remove current job from counter (successfully completed)

lock=`cat ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/.lock`

lock=$(($lock-1))

echo $lock > $lockfile



#check if jobs running

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

run_tests.sh

+15 −8
Original line number Diff line number Diff line
@@ -12,21 +12,27 @@ bash /universc/launch_universc.sh -t "10x" --setup 


## test 10x data

# unzip input data

if [[ ! -f /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/lib/python/cellranger/barcodes/3M-february-2018.txt.gz ]]; then

    gzip /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/lib/python/cellranger/barcodes/3M-february-2018.txt

fi

# test cellranger call

cellranger testrun --id="tiny-test"

# unzip input data

gunzip /universc/test/shared/cellranger-tiny-fastq/3.0.0/*fastq

gunzip /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/lib/python/cellranger/barcodes/3M-february-2018.txt.gz 

gunzip -fk /universc/test/shared/cellranger-tiny-fastq/3.0.0/*fastq.gz

gunzip -fk /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/lib/python/cellranger/barcodes/3M-february-2018.txt.gz 

# test cellranger call

cellranger count --id="tiny-count" \

 --fastqs="/cellranger-3.0.2.9001/cellranger-tiny-fastq/3.0.0/" --sample="tinygex_S1" \

 --transcriptome="/cellranger-3.0.2.9001/cellranger-tiny-ref/3.0.0/" \

 --chemistry="SC3Pv2"

cellranger count --id="tiny-count-v3" \

 --fastqs="/cellranger-3.0.2.9001/cellranger-tiny-fastq/3.0.0/" --sample="tinygex" \

 --transcriptome="/cellranger-3.0.2.9001/cellranger-tiny-ref/3.0.0"



cellranger count --id="tiny-count-v2" \

 --fastqs="/cellranger-3.0.2.9001/cellranger-tiny-fastq/1.2.0/" --sample="tinygex" \

 --transcriptome="/cellranger-3.0.2.9001/cellranger-tiny-ref/1.2.0"



# call convert on 10x with multiple lanes

bash /universc/launch_universc.sh --id "test-10x" --technology "10x" \

 --reference "/universc/test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --chemistry "SC3Pv3" \

 --file "/universc/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001" \

 "/universc/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002"
@@ -39,7 +45,8 @@ bash /universc/launch_universc.sh -t "nadia" --setup 
bash /universc/launch_universc.sh --id "test-dropseq" --technology "nadia" \

 --reference "/universc/test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --read1 "/universc/test/shared/dropseq-test/SRR1873277_S1_L001_R1_001" \

 --read2 "/universc/test/shared/dropseq-test/SRR1873277_S1_L001_R2_001" 

 --read2 "/universc/test/shared/dropseq-test/SRR1873277_S1_L001_R2_001" \

 --chemistry "SCP-V3"



## test icell8 data

# unzip input data

test/shared/mappa-test/99999_mappa_test_selected_WellList.TXT

deleted100644 → 0
+0 −9
Original line number Diff line number Diff line 
Row	Col	Candidate	For dispense	Sample	Barcode	State	Cells1	Cells2	Signal1	Signal2	Size1	Size2	Integ Signal1	Integ Signal2	Circularity1	Circularity2	Confidence	Confidence1	Confidence2	Comment	Dispense tip	Drop index	Global drop index

6	37	yes	yes	K562	CGTCGAGG+TCATGCTG	Good	1	0	390		59		23010		0.943399		1	1	1		4	159	430

44	45	yes	yes	K562	TCATACCA+GTTCGGTT	Good	1	0	489		63		30807		0.9645678		1	1	1		6	25	639

38	4	yes	yes	K562	TGGATCAA+GTTCAACT	Good	1	0	509		63		32067		0.9645678		1	1	1		1	5	176

38	53	yes	yes	K562	TGGATCAA+GTAGAATG	Good	1	0	799		27		21573		1		1	1	1		2	124	161

0	19	yes	yes	K562	AACCGGTT+TTAGGCGG	Good	1	0	504		58		29232		1		1	1	1		1	114	430

4	37	yes	yes	Pos_Ctrl	CATTCGGT+TCATGCTG	Good	1	0	411		46		18906		1		1	1	1		7	87	169

42	52	yes	yes	Pos_Ctrl	ATTCTACC+CTTCTTAC	Good	1	0	554		58		32132		1		1	1	1		1	98	150

8	4	yes	yes	K562	TATACGGA+GTTCAACT	Good	1	0	493		63		31059		0.9645678		1	1	1		8	5	101
 
 No newline at end of file

test/shared/mappa-test/mappa_barcodes.txt

0 → 100644
+8 −0
Original line number Diff line number Diff line 
CGTCGAGGTCATGCTG

TCATACCAGTTCGGTT

TGGATCAAGTTCAACT

TGGATCAAGTAGAATG

AACCGGTTTTAGGCGG

CATTCGGTTCATGCTG

ATTCTACCCTTCTTAC

TATACGGAGTTCAACT

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