Commit 619fc373 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

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

parents 94631173 bd0e3730

Dockerfile

+2 −1
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@@ -7,7 +7,8 @@ RUN apt-get update \ 
 git \

 git-lfs \

 make \

 gzip

 gzip \

 rename



RUN apt-get install -y \

  curl \

crconverter_open.sh

+1 −2
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@@ -253,8 +253,7 @@ for op in "${@}"; do 
                next=true

                shift

            else

                echo "Error: value missing for --description"

                exit 1

                description=""

            fi

            ;;

        -v|--version)

launch_universc.sh

+4 −4
Original line number Diff line number Diff line
@@ -611,12 +611,12 @@ read12=("${read1[@]}" "${read2[@]}") 
for fq in "${read12[@]}"; do

    name=`basename $fq`

    name=${name%.*}

    sn=`echo ${name} | cut -f1 -d'_'`

    ln=`echo ${name} | cut -f3 -d'_' | sed 's/L00//'`

    fields=`echo ${name} | grep -o "_" | wc -l`

    fields=$(($fields+1))

    LANE+=($ln)

    if [[ ${fields} != 5 ]]; then

    sn=`echo ${name} | cut -f1-$((${fields}-4))  -d'_'`

    lane=`echo ${name} | cut -f$((${fields}-2)) -d'_' | sed 's/L00//'`

    LANE+=($lane)

    if [[ ${fields} -le 4 ]]; then

        echo "Error: filename $fq is not following the naming convention. (e.g. EXAMPLE_S1_L001_R1_001.fastq)";

        exit 1

    elif [[ $fq != *'.fastq'* ]] && [[ $fq != *'.fq'* ]]; then

run_tests.sh

+24 −16
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@@ -4,45 +4,52 @@ cd ~ 
## check cellranger installed

cellranger count ---version



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





## check convert is installed

bash /universc/launch_universc.sh -v



# reset barcodes for test

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



## test 10x data

# unzip input data

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

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

# test cellranger call

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

 --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 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 

# 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"



# call convert on 10x with multiple lanes

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

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

 --file "/universc/test/shared/cellranger-tiny-fastq/3.0.0/tinygex"

 --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"



## test drop-seq data

# unzip input data

gunzip universc/test/shared/dropseq-test/*fastq.gz

gunzip /universc/test/shared/dropseq-test/*fastq.gz

# test manual setup

bash /universc/launch_universc.sh -t "nadia" --setup

# call on dropseq with files

bash /universc/launch_universc.sh --id "test-dropseq" --technology "nadia" \

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

 --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" 



## test icell8 data

# unzip input data

gunzip universc/test/shared/mappa-test/*fastq.gz

gunzip /universc/test/shared/mappa-test/*fastq.gz

# call on icell8 files with custom whitelist and non-standard file names

bash /universc/launch_universc.sh --id "test-icell8" --technology "iCell8" \

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

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

 --read1 "/universc/test/shared/mappa-test/test_FL_R1.fastq" \

 --read2 "/universc/test/shared/mappa-test/test_FL_R2.fastq" \

 --barcodefile "/universc/test/shared/dropseq-test/99999_mappa_test_selected_WellList.TXT"

 --barcodefile "/universc/test/shared/mappa-test/99999_mappa_test_selected_WellList.TXT"



#restore file names for test job

mv /universc/test/shared/mappa-test/test_FL_S1_L001_R1_001.fastq /universc/test/shared/mappa-test/test_FL_R1.fastq
@@ -50,5 +57,6 @@ mv /universc/test/shared/mappa-test/test_FL_S1_L001_R2_001.fastq /universc/test/ 


# compress all input files

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

gzip universc/test/shared/dropseq-test/*fastq

gzip universc/test/shared/mappa-test/*fastq
 
gzip /universc/test/shared/dropseq-test/*fastq

gzip /universc/test/shared/mappa-test/*fastq

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