Commit ac6882bb authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update testing on dockerhub

parents b7a6f4b7 9f81202d

docker-compose.test.yml

+15 −3
Original line number Diff line number Diff line 
test:

sut:

  build: .

  command: pwd

#bash run_tests.sh
 
  command: echo "build complete" && bash test/test_call.sh



test_10x:

  build: .

  command: bash test/run_tests_10x.sh



test_dropseq:

  build: .

  command: bash test/run_tests_dropseq.sh



test_icell8:

  build: .

  command: bash test/run_tests_icell8.sh

docker-compose.yml

+13 −1
Original line number Diff line number Diff line 
sut:

  build: .

  command: echo "build complete"
 
  command: echo "build complete" && bash test/test_call.sh



test_10x:

  build: .

  command: bash test/run_tests_10x.sh



test_dropseq:

  build: .

  command: bash test/run_tests_dropseq.sh



test_icell8:

  build: .

  command: bash test/run_tests_icell8.sh

launch_universc.sh

+60 −5
Original line number Diff line number Diff line
@@ -69,8 +69,15 @@ 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, chromium, nadia, dropseq, icell8, or custom)

                                e.g. custom_16_10

  -t,  --technology PLATFORM    Name of technology used to generate data.

                                Supported technologies:

                                  10x Genomics (16bp barcode, 10bp UMI): 10x, chromium (v2 or v3 automatically detected)

                                  Drop-Seq (12pb barcode, 8pm UMI): nadia, dropseq

                                  iCell8 version 3 (11bp barcode, 14bp UMI): icell8 or custom

                                  Quartz-Seq2 (14bp barcodes, 8bp UMI): quartzseq2-384

                                  Quartz-Seq2 (15bp barcodes, 8bp UMI): quartzseq2-1536                                    

                                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

  -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'
@@ -434,6 +441,15 @@ if [[ "$technology" == "dropseq" ]] || [[ "$technology" == "drop-seq" ]]; then 
    echo "Running with Nadia parameters (Drop-Seq)"

    technology="nadia"

fi

if [[ "$technology" == "quartz-seq2-384" ]] || [[ "$technology" == "quartzseq2-384" ]] || [[ "$technology" == "quartz-seq2-v3.1" ]] || [[ "$technology" == "quartzseq2-v3.1" ]] || [[ "$technology" == "quartzseq2v3.1" ]];; then

    echo "Running with Quartz-Seq2 v3.1 parameters 384 wells (14bp barcode)"

    technology="quartz-seq2-384"

fi



if [[ "$technology" == "quartz-seq2-1536" ]] || [[ "$technology" == "quartzseq2-1536" ]] || [[ "$technology" == "quartz-seq2-v3.2" ]] || [[ "$technology" == "quartzseq2-v3.2" ]] || [[ "$technology" == "quartzseq2v3.2" ]];; then

    echo "Running with Quartz-Seq2 v3.2 parameters 1536 wells (15bp barcode)"

    technology="quartz-seq2-1536"

fi



#check if technology matches expected inputs

if [[ "$technology" != "10x" ]] && [[ "$technology" != "nadia" ]] && [[ "$technology" != "icell8" ]]; then
@@ -671,11 +687,42 @@ else 
    elif [[ "$technology" == "nadia" ]]; then

        barcodefile=${SDIR}/nadia_barcode.txt

        if [[ ! -f ${barcodefile} ]]; then

            #creat a nadia barcode file

            #create a nadia barcode file

            echo "No barcodes whitelists available for Drop-Seq or Nadia: all possible barcodes accepted (valid barcodes will be 100% as a result)"

            echo {A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G} | sed 's/ /\n/g' | sort | uniq > ${barcodefile}

        fi

    elif [[ "$technology" == "icell8" ]]; then

        barcodefile=${SDIR}/iCell8_barcode.txt

    elif [[ "$technology" != "custom"* ]]; then

        custom=`echo $technology | grep -o "_" | wc -l`

        custom=$(($custom+1))

        customname=`echo $technology | cut -f1-$((${custom}-2))  -d'_'`

        barcodelength=`echo $technology | cut -f$((${custom}-1))  -d'_'`

        #check whether barcodes exceed 16bp (and reuse 16bp whitelist for all greater than 16bp)

        if [[  $barcodelength -ge 16 ]]; then

            echo "Barcode length ($barcodelength) of 16 or more:"

            echo "    ...using barcode whitelist of 16bp"

        fi

        minlength = `echo $(( $barcodelength < 16 ? $barcodelength : 16 ))`

        # compute custom barcodes if barcode length is different

        barcodefile=${SDIR}/${customname}_${minlength}_barcode.txt

        if [[ ! -f ${barcodefile} ]]; then

            echo "No barcodes whitelists available for ${customname}: all possible barcodes accepted (valid barcodes will be 100% as a result)"

            echo "***Warning: giving a barcode whitelist --barcodefile is recommended where available.***"

            if [[ -f ${SDIR}/*${barcodelength}_barcode.txt ]]

                pregeneratedfile=`ls ${SDIR}/*${barcodelength}_barcode.txt | awk '{print $1;}' | head -n 1`

                echo "$pregeneratedfile for barcode(${barcodelength}) generated already"

                ln -s $pregeneratedfile $barcodefile

                echo "    ...using this as $barcodefile"

            else

                echo "generating $barcodefile of barcode length $minlength"

                strings=`for ii in {1..${minlength}}

                             do

                             echo "{A,T,C,G}"

                             done |  tr "\n" " " | sed "s/ //g" | xargs -I {} echo {} | xargs -I {} echo {}`

                eval "echo ${strings}" | sed 's/ /\n/g' | sort | uniq > ${barcodefile}

            fi

        fi 

    fi

fi
@@ -761,9 +808,17 @@ elif [[ "$technology" == "nadia" ]]; then 
elif [[ "$technology" == "icell8" ]]; then

    barcodelength=11

    umilength=14

elif [[ "$technology" == "quartz-seq2-384" ]]; then

    barcodelength=14

    umilength=8

elif [[ "$technology" == "quartz-seq2-1536" ]]; then

    barcodelength=15

    umilength=8 

else

    barcodelength=`echo $technology | cut -f 2 -d'_'`

    umilength=`echo $technology | cut -f 3 -d'_'`

    custom=`echo $technology | grep -o "_" | wc -l`

    custom=$(($custom+1))

    barcodelength=`echo $technology | cut -f$((${custom}-1))  -d'_'`

    umilength=`echo $technology | cut -f$((${custom}))  -d'_'`

fi



#adjustment lengths

run_tests.sh→test/run_tests.sh

+0 −6
Original line number Diff line number Diff line
@@ -3,12 +3,6 @@ 
# run tests in home directory (writeable)

cd ~



## check cellranger installed

cellranger count ---version



## check convert is installed

bash /universc/launch_universc.sh -v



# reset barcodes for test

bash /universc/launch_universc.sh -t "10x" --setup

test/run_tests_10x.sh

0 → 100755
+40 −0
Original line number Diff line number Diff line 
#!/bin/bash



# run tests in home directory (writeable)

cd ~



# reset barcodes for test

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 -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-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-v3" --technology "10x" \

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

 --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"



bash /universc/launch_universc.sh --id "test-10x-v2" --technology "10x" \

 --reference "/universc/test/cellranger_reference/cellranger-tiny-ref/1.2.0" \

 --file "/universc/test/shared/cellranger-tiny-fastq/1.2.0/tinygex_S1_L001" \

 "/universc/test/shared/cellranger-tiny-fastq/1.2.0/tinygex_S1_L002"



# compress all input files

gzip -f /universc/test/shared/cellranger-tiny-fastq/3.0.0/*fastq

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