Commit ebc55103 authored by kai.b's avatar kai.b
Browse files

monir changes to the --verbose comments

parent 39c9401e

launch_universc.sh

+71 −61
Original line number Diff line number Diff line
@@ -995,13 +995,14 @@ if [[ $setup == "false" ]]; then 
fi



if [[ $verbose ]]; then

    echo "  ${#read1[@]} read1s: ${read1[@]}"

    echo "  ${#read2[@]} read2s: ${read2[@]}"

    echo " Input files prost-curation 1"

    echo "  ${#read1[@]}files - read1s: ${read1[@]}"

    echo "  ${#read2[@]}files - read2s: ${read2[@]}"

    if [[ ${#index1[@]} -gt 0 ]]; then

        echo "  ${#index1[@]} I1s: ${index1[@]}"

        echo "  ${#index1[@]}files - I1s: ${index1[@]}"

    fi

    if [[ ${#index2[@]} -gt 0 ]]; then

        echo "  ${#index2[@]} I2s: ${index2[@]}"

        echo "  ${#index2[@]}files - I2s: ${index2[@]}"

    fi

    echo "  number of these files are as expected"

fi
@@ -1101,13 +1102,14 @@ for key in ${keys[@]}; do 
done



if [[ $verbose ]]; then

    echo "  ${#read1[@]} read1s: ${read1[@]}"

    echo "  ${#read2[@]} read2s: ${read2[@]}"

    echo " Input files post-curation 2"

    echo "  ${#read1[@]}files - read1s: ${read1[@]}"

    echo "  ${#read2[@]}files - read2s: ${read2[@]}"

    if [[ ${#index1[@]} -gt 0 ]]; then

        echo "  ${#index1[@]} I1s: ${index1[@]}"

        echo "  ${#index1[@]}files - I1s: ${index1[@]}"

    fi

    if [[ ${#index2[@]} -gt 0 ]]; then

        echo "  ${#index2[@]} I2s: ${index2[@]}"

        echo "  ${#index2[@]}files -  I2s: ${index2[@]}"

    fi

    echo "  files exist, with extentions compatible with launch_universc.sh"

fi
@@ -1288,13 +1290,14 @@ for key in ${keys[@]}; do 
done



if [[ $verbose ]]; then

    echo "  ${#read1[@]} read1s: ${read1[@]}"

    echo "  ${#read2[@]} read2s: ${read2[@]}"

    echo " Input files post-curation 3"

    echo "  ${#read1[@]}files - read1s: ${read1[@]}"

    echo "  ${#read2[@]}files - read2s: ${read2[@]}"

    if [[ ${#index1[@]} -gt 0 ]]; then

        echo "  ${#index1[@]} I1s: ${index1[@]}"

        echo "  ${#index1[@]}files - I1s: ${index1[@]}"

    fi

    if [[ ${#index2[@]} -gt 0 ]]; then

        echo "  ${#index2[@]} I2s: ${index2[@]}"

        echo "  ${#index2[@]}files - I2s: ${index2[@]}"

    fi

    echo "  names of these files are compatible with launch_universc.sh"

fi
@@ -1375,13 +1378,14 @@ if [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrop-v3" ]] || [ 
fi



if [[ $verbose ]]; then

    echo "  ${#read1[@]} read1s: ${read1[@]}"

    echo "  ${#read2[@]} read2s: ${read2[@]}"

    echo " Input files post-curation 4"

    echo "  ${#read1[@]}files - read1s: ${read1[@]}"

    echo "  ${#read2[@]}files - read2s: ${read2[@]}"

    if [[ ${#index1[@]} -gt 0 ]]; then

        echo "  ${#index1[@]} I1s: ${index1[@]}"

        echo "  ${#index1[@]}files - I1s: ${index1[@]}"

    fi

    if [[ ${#index2[@]} -gt 0 ]]; then

        echo "  ${#index2[@]} I2s: ${index2[@]}"

        echo "  ${#index2[@]}files -  I2s: ${index2[@]}"

    fi

    echo "  input files adjusted for technology-specific conditions"

fi
@@ -1399,12 +1403,12 @@ elif [[ ${#index1[@]} -gt 0 ]]; then 
fi



if [[ $verbose ]]; then

    echo "reads:" ${read12[@]}

    echo "files to be curated:" ${read12[@]}

fi



for fq in "${read12[@]}"; do

    if [[ $verbose ]]; then

        echo "read: $fq"

        echo " read file: $fq"

    fi

    name=`basename $fq`

    name=${name%.*}
@@ -1429,13 +1433,16 @@ for fq in "${read12[@]}"; do 
        exit 1

    fi

    

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

       echo "SAMPLE: $SAMPLE"

       echo "sample (field): $sn"

    if [[ $verbose ]]; then

        echo "  $sn(extracted from file) <- $fq"

        echo "  SAMPLE NAME: $SAMPLE"

    fi



    if [[ ${sn} != $SAMPLE ]]; then

        if [[ -z $SAMPLE ]]; then

            if [[ $verbose ]]; then

                echo "  setting SAMPLE NAME to ${sn}"

            fi

            SAMPLE=${sn}

        else

            echo "Error: some samples are labeled $SAMPLE while others are labeled $sn. cellranger can only handle files from one sample at a time."
@@ -1584,7 +1591,7 @@ fi 






#####check if reference is present#####

####check if reference is present#####

if [[ -z $reference ]]; then

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

        echo "Error: option --reference is required";
@@ -1687,6 +1694,7 @@ crIN=${crIN}_${id} 
##########







#####checking if crIN exists#####

if [[ ! -d $crIN ]]; then

    convert=true
@@ -1859,6 +1867,7 @@ if [[ $lock -eq 0 ]]; then 
            sed -i "s/assert np.array_equal(in_mc.get_barcodes(), barcodes)/#assert np.array_equal(in_mc.get_barcodes(), barcodes)/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/molecule_counter.py

        fi

    fi

    

    #backup 10x navbar

    if [[ ! -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.backup.html ]];then

        cp ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.html ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.backup.html
@@ -1872,6 +1881,7 @@ if [[ $lock -eq 0 ]]; then 
        if [[ -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.backup.html ]];then

            cp ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.backup.html ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.html

        fi

        

        #restore cloupe generation

        if [[ $verbose ]]; then

            echo "restore cloupe"
@@ -1886,6 +1896,7 @@ if [[ $lock -eq 0 ]]; then 
            echo "sed -i '/out cloupe *cloupe/ {s/^#*#//g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro"

        fi

        sed -i '/out cloupe *cloupe/ {s/^#*#//g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro

        

        #restore 11 lines for cloupe preprocess call (all following steps are needed to be called together or the call will break)

        ##restore defining CLOUPE_PREPROCESS

        if [[ $verbose ]]; then
@@ -1896,8 +1907,7 @@ if [[ $lock -eq 0 ]]; then 
        sed -i '/output_for_cloupe/s/^#*#//g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro 

        ##remove calling CLOUPE_PREPROCESS

        ### iterate over all files calling CLOUPE_PREPROCESS

        for file in $(grep -l  "call CLOUPE_PREPROCESS"  ${cellrangerpath}-cs/${cellrangerversion}/mro/*.mro )

        do

        for file in $(grep -l  "call CLOUPE_PREPROCESS"  ${cellrangerpath}-cs/${cellrangerversion}/mro/*.mro ); do

            #find  start of CLOUPE_PREPROCESS call

            num=$(grep -n "call CLOUPE_PREPROCESS" $file |  head -n 1 | cut -d":" -f1)

            #find end of CLOUPE_PREPROCESS call
@@ -1913,6 +1923,7 @@ if [[ $lock -eq 0 ]]; then 
            #line of HTML in header is removed

            sed '/class="logo"/d' ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.backup.html > ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/webshim/template/navbar.html

        fi

        

        #disable cloupe generation

        if [[ $verbose ]]; then

            echo "disable cloupe"
@@ -2325,7 +2336,6 @@ else 
            

            #returns a combined R1 file with I1-I2-R1 concatenated (I1 and I2 are R1 barcode)

            mv $crIN/Concatenated_File.fastq ${convR1}



        done

    fi

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