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ignore project postfix #41

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merged 1 commit into from
Nov 21, 2024
Merged

ignore project postfix #41

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12 changes: 6 additions & 6 deletions bin/ParseDarwinSamplesheet.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand All @@ -144,15 +144,15 @@ 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")"
_fileType='VCF'

### 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} ${_filePath}, set _fileType to VCF
Expand Down Expand Up @@ -180,7 +180,7 @@ fetch_data () {
fi
elif [[ "${_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 "${_searchPath[0]}" ]]
then
Expand All @@ -192,7 +192,7 @@ fetch_data () {
elif [[ ! -d "${_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]}")"
Expand Down