Commit f749ed07 authored by kai.b's avatar kai.b
Browse files

minor bug fixes

parents b12f3d3b 007cf206

launch_universc.sh

+16 −1
Original line number Diff line number Diff line
@@ -828,6 +828,9 @@ fi 


#####Input file curation 2: Check R1, R2, I1, and I2 files for their extensions#####

##allows incomplete file names and processing compressed files

if [[ $verbose ]]; then

    echo "key: ${keys[@]}"

fi

for key in ${keys[@]}; do

    readkey=$key

    list=()
@@ -1114,7 +1117,14 @@ elif [[ ${#index1[@]} -gt 0 ]]; then 
    read12=("${read1[@]}" "${read2[@]}" "${index1[@]}")

fi



if [[ $verbose ]]; then

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

fi



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

    if [[ $verbose ]]; then

        echo "read: $fq"

    fi

    name=`basename $fq`

    name=${name%.*}

    fields=`echo ${name} | grep -o "_" | wc -l`
@@ -1133,6 +1143,11 @@ for fq in "${read12[@]}"; do 
	exit 1

    fi



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

       echo "SAMPLE: $SAMPLE"

       echo "sample (field): $sn"

    fi



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

        if [[ -z $SAMPLE ]]; then

            SAMPLE=${sn}

test/cellranger_reference/cellranger-tiny-ref/1.2.0/reference.json

LFS
+17 −3
Original line number Diff line number Diff line 
version https://git-lfs.github.com/spec/v1

oid sha256:394e690da7291c3aa40a76d111ce204230363b55ad0d8cfee04ca3f06886fb7e

size 385
 
{

    "fasta_hash": "332a9359e2b8dc662910106dd439c2b4e5e58022", 

    "genomes": [

        "hg19_chr21"

    ], 

    "gtf_hash": "b40de17097f46e3e8648bc38cfd0f2d7ebde00da", 

    "input_fasta_files": [

        "genome.fa"

    ], 

    "input_gtf_files": [

        "genes.gtf"

    ], 

    "mem_gb": 4, 

    "mkref_version": "4009.1.79-50-ge2da5f0", 

    "threads": 1, 

    "version": null

}
 
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