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Merge pull request #152 from RoanKanninga/master
new style generate_template
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,94 +1,109 @@ | ||
| #!/bin/bash | ||
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| module load NGS_DNA/3.4.1 | ||
| module list | ||
| HOST=$(hostname -s) | ||
| thisDir=$(pwd) | ||
| module list | ||
| host=$(hostname -s) | ||
| environmentParameters="parameters_${host}" | ||
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| function showHelp() { | ||
| # | ||
| # Display commandline help on STDOUT. | ||
| # | ||
| cat <<EOH | ||
| =============================================================================================================== | ||
| Script to copy (sync) data from a succesfully finished analysis project from tmp to prm storage. | ||
| Usage: | ||
| $(basename $0) OPTIONS | ||
| Options: | ||
| -h Show this help. | ||
| -a sampleType (DNA or RNA) (default=DNA) | ||
| -b build (default=b37) | ||
| -c batch (_chr or _small) (default=_chr) | ||
| -g group (default=basename of ../../../ ) | ||
| -p project (default=basename of this directory) | ||
| -r runID (default=run01) | ||
| -s species (default=homo_sapiens) | ||
| -t tmpDirectory (default=basename of ../../ ) | ||
| -w workdir (default=/groups/\${group}/\${tmpDirectory}) | ||
| =============================================================================================================== | ||
| EOH | ||
| trap - EXIT | ||
| exit 0 | ||
| } | ||
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| while getopts "t:g:w:p:r:s:b:c:h" opt; | ||
| do | ||
| case $opt in h)showHelp;; t)tmpDirectory="${OPTARG}";; g)group="${OPTARG}";; w)workDir="${OPTARG}";; p)project="${OPTARG}";; r)runID="${OPTARG}";; s)species="${OPTARG}";; b)build="${OPTARG}";; c)batch="${OPTARG}";; | ||
| esac | ||
| done | ||
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| if [[ -z "${tmpDirectory:-}" ]]; then tmpDirectory=$(basename $(cd ../../ && pwd )) ; fi ; echo "tmpDirectory=${tmpDirectory}" | ||
| if [[ -z "${group:-}" ]]; then group=$(basename $(cd ../../../ && pwd )) ; fi ; echo "group=${group}" | ||
| if [[ -z "${workDir:-}" ]]; then workDir="/groups/${group}/${tmpDirectory}" ; fi ; echo "workDir=${workDir}" | ||
| if [[ -z "${project:-}" ]]; then project=$(basename $(pwd )) ; fi ; echo "project=${project}" | ||
| if [[ -z "${runID:-}" ]]; then runID="run01" ; fi ; echo "runID=${runID}" | ||
| if [[ -z "${species:-}" ]]; then species="homo_sapiens" ; fi ; echo "species=${species}" | ||
| if [[ -z "${build:-}" ]]; then build="b37" ; fi ; echo "build=${build}" | ||
| if [[ -z "${batch:-}" ]]; then batch="_chr"; fi ; echo "batch=${batch}" | ||
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| ENVIRONMENT_PARAMETERS="parameters_${HOST}.csv" | ||
| TMPDIRECTORY=$(basename $(cd ../../ && pwd )) | ||
| GROUP=$(basename $(cd ../../../ && pwd )) | ||
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| PROJECT=projectXX | ||
| WORKDIR="/groups/${GROUP}/${TMPDIRECTORY}" | ||
| RUNID=runXX | ||
| SPECIES="homo_sapiens" | ||
| BUILD="b37" | ||
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| ## Normal user, please leave BATCH at _chr | ||
| ## For expert modus: small batchsize (6) fill in '_small' or per chromosome fill in _chr | ||
| BATCH="_chr" | ||
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| GENSCRIPTS="${WORKDIR}/generatedscripts/${PROJECT}" | ||
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| samplesheet=${GENSCRIPTS}/${PROJECT}.csv | ||
| mac2unix $samplesheet | ||
| genScripts="${workDir}/generatedscripts/${project}/" | ||
| samplesheet="${genScripts}/${project}.csv" ; mac2unix "${samplesheet}" | ||
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| python ${EBROOTNGS_DNA}/scripts/samplesize.py ${samplesheet} $thisDir | ||
| SAMPLESIZE=$(cat externalSampleIDs.txt | uniq | wc -l) | ||
| python "${EBROOTNGS_DNA}/scripts/samplesize.py" "${samplesheet}" $(pwd) | ||
| sampleSize=$(cat externalSampleIDs.txt | uniq | wc -l) | ||
| echo "Samplesize is ${sampleSize}" | ||
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| python ${EBROOTNGS_DNA}/scripts/gender.py $samplesheet | ||
| var=$(cat ${samplesheet}.tmp | wc -l) | ||
| python "${EBROOTNGS_DNA}/scripts/gender.py" "${samplesheet}" | ||
| var=$(cat "${samplesheet}.tmp" | wc -l) | ||
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| if [ $var != 0 ] | ||
| if [ "${var}" != 0 ] | ||
| then | ||
| mv ${samplesheet}.tmp ${samplesheet} | ||
| mv "${samplesheet}.tmp" "${samplesheet}" | ||
| echo "samplesheet updated with Gender column" | ||
| fi | ||
| echo "Samplesize is $SAMPLESIZE" | ||
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| if [ $SAMPLESIZE -gt 199 ] | ||
| if [ $sampleSize -gt 199 ] | ||
| then | ||
| WORKFLOW=${EBROOTNGS_DNA}/workflow_samplesize_bigger_than_200.csv | ||
| workflow=${EBROOTNGS_DNA}/workflow_samplesize_bigger_than_200.csv | ||
| else | ||
| WORKFLOW=${EBROOTNGS_DNA}/workflow.csv | ||
| fi | ||
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| if [ -f .compute.properties ]; | ||
| then | ||
| rm .compute.properties | ||
| fi | ||
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| if [ -f ${GENSCRIPTS}/out.csv ]; | ||
| then | ||
| rm -rf ${GENSCRIPTS}/out.csv | ||
| workflow=${EBROOTNGS_DNA}/workflow.csv | ||
| fi | ||
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| echo "tmpName,${TMPDIRECTORY}" > ${GENSCRIPTS}/tmpdir_parameters.csv | ||
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| perl ${EBROOTNGS_DNA}/scripts/convertParametersGitToMolgenis.pl ${GENSCRIPTS}/tmpdir_parameters.csv > \ | ||
| ${GENSCRIPTS}/tmpdir_parameters_converted.csv | ||
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| perl ${EBROOTNGS_DNA}/scripts/convertParametersGitToMolgenis.pl ${EBROOTNGS_DNA}/parameters.csv > \ | ||
| ${GENSCRIPTS}/out.csv | ||
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| perl ${EBROOTNGS_DNA}/scripts/convertParametersGitToMolgenis.pl ${EBROOTNGS_DNA}/parameters_${GROUP}.csv > \ | ||
| ${GENSCRIPTS}/group_parameters.csv | ||
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| perl ${EBROOTNGS_DNA}/scripts/convertParametersGitToMolgenis.pl ${EBROOTNGS_DNA}/${ENVIRONMENT_PARAMETERS} > \ | ||
| ${GENSCRIPTS}/environment_parameters.csv | ||
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| sh $EBROOTMOLGENISMINCOMPUTE/molgenis_compute.sh \ | ||
| -p ${GENSCRIPTS}/out.csv \ | ||
| -p ${GENSCRIPTS}/group_parameters.csv \ | ||
| -p ${GENSCRIPTS}/environment_parameters.csv \ | ||
| -p ${GENSCRIPTS}/tmpdir_parameters_converted.csv \ | ||
| -p ${EBROOTNGS_DNA}/batchIDList${BATCH}.csv \ | ||
| -p ${GENSCRIPTS}/${PROJECT}.csv \ | ||
| -w ${EBROOTNGS_DNA}/create_in-house_ngs_projects_workflow.csv \ | ||
| -rundir ${GENSCRIPTS}/scripts \ | ||
| --runid ${RUNID} \ | ||
| -o "workflowpath=${WORKFLOW};\ | ||
| outputdir=scripts/jobs;mainParameters=${GENSCRIPTS}/out.csv;\ | ||
| group_parameters=${GENSCRIPTS}/group_parameters.csv;\ | ||
| groupname=${GROUP};\ | ||
| if [ -f "${genScripts}/out.csv" ];then rm -rf "${genScripts}/out.csv" ; fi | ||
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| echo "tmpName,${tmpDirectory}" > ${genScripts}/tmpdir_parameters.csv | ||
| perl "${EBROOTNGS_DNA}/scripts/convertParametersGitToMolgenis.pl" "${genScripts}/tmpdir_parameters.csv" > "${genScripts}/tmpdir_parameters_converted.csv" | ||
| perl "${EBROOTNGS_DNA}/scripts/convertParametersGitToMolgenis.pl" "${EBROOTNGS_DNA}/parameters.csv" > "${genScripts}/out.csv" | ||
| perl "${EBROOTNGS_DNA}/scripts/convertParametersGitToMolgenis.pl" "${EBROOTNGS_DNA}/parameters_${group}.csv" > "${genScripts}/group_parameters.csv" | ||
| perl "${EBROOTNGS_DNA}/scripts/convertParametersGitToMolgenis.pl" "${EBROOTNGS_DNA}/${environmentParameters}.csv" > "${genScripts}/environment_parameters.csv" | ||
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| echo "BATCHIDLIST=${EBROOTNGS_DNA}/batchIDList${batch}.csv" | ||
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| sh "${EBROOTMOLGENISMINCOMPUTE}/molgenis_compute.sh" \ | ||
| -p "${genScripts}/out.csv" \ | ||
| -p "${genScripts}/group_parameters.csv" \ | ||
| -p "${genScripts}/environment_parameters.csv" \ | ||
| -p "${genScripts}/tmpdir_parameters_converted.csv" \ | ||
| -p "${EBROOTNGS_DNA}/batchIDList${batch}.csv" \ | ||
| -p "${genScripts}/${project}.csv" \ | ||
| -w "${EBROOTNGS_DNA}/create_in-house_ngs_projects_workflow.csv" \ | ||
| -rundir "${genScripts}/scripts" \ | ||
| --runid "${runID}" \ | ||
| -o workflowpath="${workflow};\ | ||
| outputdir=scripts/jobs;mainParameters=${genScripts}/out.csv;\ | ||
| group_parameters=${genScripts}/group_parameters.csv;\ | ||
| groupname=${group};\ | ||
| ngsversion=$(module list | grep -o -P 'NGS_DNA(.+)');\ | ||
| environment_parameters=${GENSCRIPTS}/environment_parameters.csv;\ | ||
| tmpdir_parameters=${GENSCRIPTS}/tmpdir_parameters_converted.csv;\ | ||
| batchIDList=${EBROOTNGS_DNA}/batchIDList${BATCH}.csv;\ | ||
| worksheet=${GENSCRIPTS}/${PROJECT}.csv" \ | ||
| environment_parameters=${genScripts}/environment_parameters.csv;\ | ||
| tmpdir_parameters=${genScripts}/tmpdir_parameters_converted.csv;\ | ||
| batchIDList=${EBROOTNGS_DNA}/batchIDList${batch}.csv;\ | ||
| worksheet=${genScripts}/${project}.csv" \ | ||
| -weave \ | ||
| --generate | ||
|
|
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