diff --git a/bin/ParseDarwinSamplesheet.sh b/bin/ParseDarwinSamplesheet.sh index 2b76d56..c75f3f0 100755 --- a/bin/ParseDarwinSamplesheet.sh +++ b/bin/ParseDarwinSamplesheet.sh @@ -122,13 +122,13 @@ fetch_data () { _projectId="${_projectId::-1}" fi - log4Bash 'WARN' "${LINENO}" "${FUNCNAME[0]:-main}" '0' "Try to find: /groups/${NGSGROUP}/prm0"*"/projects/${_projectId}"*"${_postfix}" + log4Bash 'WARN' "${LINENO}" "${FUNCNAME[0]:-main}" '0' "Try to find: /groups/${NGSGROUP}/prm0"*"/projects/${_projectId}"* if [[ "${_prefix}" =~ ^(NGS|NGSR|QXTR|XHTS|MAGR|QXT|HSR|GS)$ ]] && [[ "${_type}" =~ ^(WES|WGS)$ ]] then ### - _searchPath=("/groups/${NGSGROUP}/prm0"*"/projects/${_projectId}"*"${_postfix}/run01/results/alignment/") + _searchPath=("/groups/${NGSGROUP}/prm0"*"/projects/${_projectId}"*"/run01/results/alignment/") if [[ -e "${_searchPath[0]}" ]] then @@ -144,7 +144,7 @@ fetch_data () { fi elif [[ ! -d "${_searchPath[0]}" ]] then - _searchPath=("/groups/${NGSGROUP}/prm0"*"/projects/${_projectId}"*"${_postfix}/run01/results/concordanceCheckSnps/") + _searchPath=("/groups/${NGSGROUP}/prm0"*"/projects/${_projectId}"*"/run01/results/concordanceCheckSnps/") #fetch filename and path, and store in ${_sampleId} ${_filePath}, set _fileType to VCF _filePath="$(set -e; fetch "${_sample}" ".concordanceCheckCalls.vcf" "${_searchPath[0]}")" _sampleId="$(basename "${_filePath}" ".concordanceCheckCalls.vcf")" @@ -152,7 +152,7 @@ fetch_data () { ### later switch vcf before bam. -# _searchPath=("/groups/${NGSGROUP}/prm0"*"/projects/${_project}"*"/run01/results/concordanceCheckSnps/") +# _searchPath=("/groups/${NGSGROUP}/prm0"*"/projects/${_projectId}"*"/run01/results/concordanceCheckSnps/") # if [[ -e "${_searchPath[0]}" ]] # then # #fetch filename and path, and store in ${_sampleId} ${_filePath}, set _fileType to VCF @@ -180,7 +180,7 @@ fetch_data () { fi elif [[ "${_project}" == "GS_"* ]] && [[ "${_type}" == "RNASeq" ]] then - _searchPath=("/groups/${NGSGROUP}/prm0"*"/projects/${_projectId}"*"${_postfix}/run01/results/variants/concordance/") + _searchPath=("/groups/${NGSGROUP}/prm0"*"/projects/${_projectId}"*"/run01/results/variants/concordance/") if [[ -d "${_searchPath[0]}" ]] then @@ -192,7 +192,7 @@ fetch_data () { elif [[ ! -d "${_searchPath[0]}" ]] then log4Bash 'INFO' "${LINENO}" "${FUNCNAME[0]:-main}" '0' "RNA VCF not found, Try fetching BAM." - _searchPath=("/groups/${NGSGROUP}/prm0"*"/projects/${_projectId}"*"${_postfix}/run01/results/alignment/") + _searchPath=("/groups/${NGSGROUP}/prm0"*"/projects/${_projectId}"*"/run01/results/alignment/") #fetch filename and path, and store in ${_sampleId} ${_filePath}, set _fileType to CRAM _filePath="$(set -e; fetch "${_sample}" ".sorted.merged.bam" "${_searchPath[0]}")"