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Merge pull request #216 from kdelange/master
script to make sample sheet for inhouse research samples
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| #!/bin/bash | ||
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| set -e | ||
| set -u | ||
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| function showHelp() { | ||
| # | ||
| # Display commandline help on STDOUT. | ||
| # | ||
| cat <<EOH | ||
| =============================================================================================================== | ||
| Usage: | ||
| $(basename $0) OPTIONS | ||
| Options: | ||
| --h Show this help. | ||
| Required: | ||
| -p projectName | ||
| -d sequencingStartDate (YYMMDD) | ||
| -r run (run number contains 4 numbers: 0123) | ||
| -f flowcell (example: NextSeq, AHLJ5YAFXX or MiSeq, 000000000-BPJ2D_projectName) | ||
| -q sequencer (NextSeq:NB501043/NB501093 or MiSeq:M01785/M01997) | ||
| -l lane (number of lanes used, 1 for MiSeq, 4 for NextSeq) | ||
| Optional: | ||
| -w workDir (default is this directory) | ||
| -b barcodeType (default: RPI. AGI,LEX, NEB enz.) | ||
| -c capturingKit (default:None, name of capturingKit (e.g. Agilent\/ONCO_v3) | ||
| -k prepKit (default:Exceptional Prep kit. Important for RNA: lexogen, TruSeq, RiboZero) | ||
| -g species (default:homo_sapiens|GRCh37, if other species, supply like 'homo_sapiens|GRCh37') | ||
| -s sampleType (DNA/RNA, default:RNA) | ||
| -t seqType (default:PE. otherwise specify SR) | ||
| -i informationFile (default:None. Comma separated txt file, 1st column barcode, 2nd colum externalSampleID. NO HEADER!) | ||
| -n sampleNumber (Number of samples in the pool, only necessary if no informationFile is provided) | ||
| Output will be written in workDir with the name: {projectName}.csv | ||
| =============================================================================================================== | ||
| EOH | ||
| trap - EXIT | ||
| exit 0 | ||
| } | ||
| sequencingStartdate= | ||
| while getopts "w:s:k:t:g:q:l:m:p:c:d:r:f:b:n:i:h" opt; | ||
| do | ||
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| case $opt in h)showHelp;; | ||
| w)workDir="${OPTARG}";; | ||
| s)sampleType="${OPTARG}";; | ||
| k)prepKit="${OPTARG}";; | ||
| t)seqType="${OPTARG}";; | ||
| g)species="${OPTARG}";; | ||
| q)sequencer="${OPTARG}";; | ||
| l)lane="${OPTARG}";; | ||
| p)projectName="${OPTARG}";; | ||
| c)capturingKit="${OPTARG}";; | ||
| d)sequencingStartDate="${OPTARG}";; | ||
| r)run="${OPTARG}";; | ||
| f)flowcell="${OPTARG}";; | ||
| b)barcodeType="${OPTARG}";; | ||
| n)sampleNumber="${OPTARG}";; | ||
| i)informationFile="${OPTARG}";; | ||
| esac | ||
| done | ||
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| if [[ -z "${sampleType:-}" ]]; then | ||
| sampleType="RNA" | ||
| fi | ||
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| if [[ -z "${capturingKit:-}" ]]; then | ||
| capturingKit="None" | ||
| fi | ||
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| if [[ -z "${projectName:-}" ]]; then | ||
| echo -e '\nERROR: Must specify a projectName\n' | ||
| exit 1 | ||
| fi | ||
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| if [[ -z "${sequencingStartDate:-}" ]]; then | ||
| echo -e '\n ERROR: must specify sequencingStartDate YYMMDD' | ||
| exit 1 | ||
| fi | ||
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| if [[ -z "${seqType:-}" ]]; then | ||
| seqType="PE" | ||
| fi | ||
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| if [[ -z "${prepKit:-}" ]]; then | ||
| prepKit="'Exceptional Prep kit'" | ||
| fi | ||
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| if [[ -z "${workDir:-}" ]]; then | ||
| workDir=$(pwd) | ||
| fi | ||
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| if [[ -z "${species:-}" ]]; then | ||
| species="homo_sapiens|GRCh37" | ||
| fi | ||
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| if [[ -z "${sequencer:-}" ]]; then | ||
| echo -e '\n ERROR: must specify sequencer used' | ||
| exit 1 | ||
| fi | ||
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| if [[ -z "${run:-}" ]]; then | ||
| echo -e '\n ERROR: must specify run number, like 0123' | ||
| exit 1 | ||
| fi | ||
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| if [[ -z "${lane:-}" ]]; then | ||
| echo -e '\n ERROR: must specify numbers of lanes used' | ||
| exit 1 | ||
| fi | ||
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| if [[ -z "${flowcell:-}" ]]; then | ||
| echo -e '\n ERROR: must specify flowcell number' | ||
| exit 1 | ||
| fi | ||
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| if [[ -z "${barcodeType:-}" ]]; then | ||
| barcodeType="RPI" | ||
| fi | ||
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| if [[ -z "${sampleNumber:-}" ]]; then | ||
| sampleNumber="" | ||
| fi | ||
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| if [[ -z "${informationFile:-}" ]]; then | ||
| informationFile="None" | ||
| fi | ||
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| printf "externalSampleID,barcode,project,capturingKit,sampleType,seqType,prepKit,species,Gender,arrayFile,lane,sequencingStartDate,sequencer,run,flowcell\n" > "${workDir}/${projectName}.csv" | ||
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| if [ "${informationFile}" == "None" ]; then | ||
| for ((l=1;l<="${lane}";l++)) | ||
| do | ||
| for ((i=1;i<="${SampleNumber}";i++)) | ||
| do | ||
| printf "${projectName}_sample${i}" >> "${workDir}/${projectName}.csv" ##Dummy external sample ID | ||
| printf ",DummyBarcode${i}" >> "${workDir}/${projectName}.csv" ## Dummy barcode | ||
| printf ",${projectName}" >> "${workDir}/${projectName}.csv" ## project | ||
| printf ",${capturingKit}" >> "${workDir}/${projectName}.csv" ## capturingKit | ||
| printf ",${sampleType}" >> "${workDir}/${projectName}.csv" ## sampleType | ||
| printf ",${seqType}" >> "${workDir}/${projectName}.csv" ## seqType | ||
| printf ",${prepKit}" >> "${workDir}/${projectName}.csv" ## prepKit | ||
| printf ",${species}" >> "${workDir}/${projectName}.csv" ## species | ||
| printf "," >> "${workDir}/${projectName}.csv" ## Gender | ||
| printf "," >> "${workDir}/${projectName}.csv" ## arrayFile | ||
| printf ",${l}" >> "${workDir}/${projectName}.csv" ##lane | ||
| printf ",${sequencingStartDate}" >> "${workDir}/${projectName}.csv" ##sequencingstartdate | ||
| printf ",${sequencer}" >> "${workDir}/${projectName}.csv" ##sequencer | ||
| printf ",${run}" >> "${workDir}/${projectName}.csv" ##run | ||
| printf ",${flowcell}\n" >> "${workDir}/${projectName}.csv" ## flowcell | ||
| done | ||
| done | ||
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| else | ||
| for ((l=1;l<="${lane}";l++)) | ||
| do | ||
| while read line | ||
| do | ||
| barcode=$(echo "${line}" | cut -d , -f1) | ||
| externalSampleID=$(echo "${line}" | cut -d , -f2) | ||
| printf "${externalSampleID}" >> "${workDir}/${projectName}.csv" ##external sample ID | ||
| printf ",${barcode}" >> "${workDir}/${projectName}.csv" ## barcode | ||
| printf ",${projectName}" >> "${workDir}/${projectName}.csv" ## project | ||
| printf ",${capturingKit}" >> "${workDir}/${projectName}.csv" ## capturingKit | ||
| printf ",${sampleType}" >> "${workDir}/${projectName}.csv" ## sampleType | ||
| printf ",${seqType}" >> "${workDir}/${projectName}.csv" ## seqType | ||
| printf ",${prepKit}" >> "${workDir}/${projectName}.csv" ## prepKit | ||
| printf ",${species}" >> "${workDir}/${projectName}.csv" ## species | ||
| printf "," >> "${workDir}/${projectName}.csv" ## Gender | ||
| printf "," >> "${workDir}/${projectName}.csv" ## arrayFile | ||
| printf ",${l}" >> "${workDir}/${projectName}.csv" ##lane | ||
| printf ",${sequencingStartDate}" >> "${workDir}/${projectName}.csv" ##sequencingstartdate | ||
| printf ",${sequencer}" >> "${workDir}/${projectName}.csv" ##sequencer | ||
| printf ",${run}" >> "${workDir}/${projectName}.csv" ##run | ||
| printf ",${flowcell}\n" >> "${workDir}/${projectName}.csv" ## flowcell | ||
| done < "${informationFile}" | ||
| done | ||
| fi | ||
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| echo "Samplesheet is finished!" | ||
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