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stereoPipeline_v7.1_manual_part2.sh
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#!/bin/bash
set -e
if [[ $# -lt 12 ]];then
echo "usage: sh $0 -SN -dataDir -registJson -speciesName -tissueType -outDir -imageRecordFile -imageCompressedFile -doCellBin -threads -sif
-SN : sample id
-dataDir : output directory of gene expression matrix result
-registJson : manual registration json file
-speciesName : specie of the sample
-tissueType : tissue type of the sample
-outDir : output directory path (Suggest not being in the same directory as the dataDir directory)
-imageRecordFile : QC-success: image file(*.ipr) found in /dataDir/03.register; QC-failed: image file(*.ipr) generated by ImageStudio software
-imageCompressedFile : image file(*.tar.gz) generated by ImageStudio software
-doCellBin : [Y/N]
-threads : the number of threads to be used in running the pipeline
-sif : the file format of the visual software
"
exit
fi
while [[ -n "$1" ]]
do
case "$1" in
-SN) SN="$2"
shift ;;
-dataDir) dataDir="$2"
shift ;;
-registJson) registJson="$2"
shift ;;
-speciesName) refName="$2"
shift ;;
-tissueType) tissueType="$2"
shift ;;
-outDir) outDir="$2"
shift ;;
-imageRecordFile) iprFile="$2"
shift ;;
-imageCompressedFile) imageTarFile="$2"
shift ;;
-doCellBin) doCell="$2"
shift ;;
-threads) threads="$2"
shift ;;
-sif) sif="$2"
shift ;;
esac
shift
done
# Software check
if [ `command -v singularity` ]
then
singularityPath=`command -v singularity`
echo `date` " singularity check: pass, and singularity path is ${singularityPath}"
else
echo `date` " singularity check: singularity does not exits, please verify that you have installed singularity and exported it to your system PATH variable"
exit
fi
if [[ -n $sif ]]
then
echo `date` " singularity image file check: file exist and SIF path is ${sif}"
else
echo `date` " singularity image file check: file does not exist, please double check your SIF file is in the current directory or the path given by the option -s is valid."
fi
# Get summary of previous gene expression matrix result
barcodeReadsCounts=${dataDir}/01.merge/${SN}.merge.barcodeReadsCount.txt
starBams=()
bcStat=()
bcFinalOut=()
bcReadsCounts=()
for bam in `find $dataDir -name \*.Aligned.sortedByCoord.out.bam`;do starBams[${#starBams[@]}]=$bam;done
for cidstat in `find $dataDir -name \*CIDMap.stat`;do bcStat[${#bcStat[@]}]=$cidstat;done
for logfinalout in `find $dataDir -name \*.Log.final.out`;do bcFinalOut[${#bcFinalOut[@]}]=$logfinalout;done
for bccount in `find $dataDir -name \*barcodeReadsCount.txt`;do bcReadsCounts[${#bcReadsCounts[@]}]=$bccount;done
if [[ $(echo ${#bcReadsCounts[*]}) == '1' ]]; then
bcReadsCountsStr=$bcReadsCounts
starBamsStr=${starBams[0]}
bcFinalOutStr=${bcFinalOut[0]}
bcStatStr=${bcStat[0]}
else
bcReadsCountsStr=$( IFS=','; echo "${bcReadsCounts[*]}" )
starBamsStr=$( IFS=','; echo "${starBams[*]}" )
bcFinalOutStr=$( IFS=','; echo "${bcFinalOut[*]}" )
bcStatStr=$( IFS=','; echo "${bcStat[*]}" )
fi
# Get basic information from JSON
offsetX=`cat ${registJson} | sed 's/,/\n/g' | grep "offsetX" | sed 's/:/\n/g' | sed '1d' | sed 's/}//g'|sed 's/"//g'`
offsetY=`cat ${registJson} | sed 's/,/\n/g' | grep "offsetY" | sed 's/:/\n/g' | sed '1d' | sed 's/}//g'|sed 's/"//g'`
flip=`cat ${registJson} | sed 's/,/\n/g' | grep "flip" | sed 's/:/\n/g' | sed '1d' | sed 's/}//g'|sed 's/"//g'`
rotate=`cat ${registJson} | sed 's/,/\n/g' | grep "rotate" | sed 's/:/\n/g' | sed '1d' | sed 's/}//g'|sed 's/"//g'`
isTunedStr=`cat ${registJson} | sed 's/,/\n/g' | grep "isTuned" | sed 's/:/\n/g' | sed '1d' | sed 's/}//g'|sed 's/"//g'`
extrude_x=`cat ${registJson} | sed 's/,/\n/g' | grep "extrude_x" | sed 's/:/\n/g' | sed '1d' | sed 's/}//g'|sed 's/"//g'`
extrude_y=`cat ${registJson} | sed 's/,/\n/g' | grep "extrude_y" | sed 's/:/\n/g' | sed '1d' | sed 's/}//g'|sed 's/"//g'`
if [[ isTunedStr == 'true' ]];then isTuned='True';else isTuned='False';fi
# Prepare output directories
if [[ $iprFile ]] && [[ $imageTarFile ]];then
iprDIR=$(dirname $iprFile)
imgTarDIR=$(dirname $imageTarFile)
fi
if [[ ! -d $outDir ]];then
mkdir -p $outDir
fi
result_03register=${outDir}/03.register
result_04tissuecut=${outDir}/04.tissuecut
result_05spatialcluster=${outDir}/05.spatialcluster
result_06saturation=${outDir}/06.saturation
result_07report=${outDir}/07.report
result_visualization=${outDir}/visualization
arr_result=( $result_04tissuecut $result_05spatialcluster $result_06saturation $result_07report $result_visualization)
for each in "${arr_result[@]}";
do
mkdir -p $each
done
if [[ ! -d $result_03register ]];then
mkdir -p $result_03register
fi
if [[ $doCell == "Y" ]]; then
result_041cellcut=${outDir}/041.cellcut
result_051cellcluster=${outDir}/051.cellcluster
mkdir -p $result_041cellcut
mkdir -p $result_051cellcluster
fi
## Get original TIFF path, either QCPass or QCFail
if [[ ! -d $dataDir/03.register/manual_register ]];then
tifDir=$dataDir/03.register
else
tifDir=$dataDir/03.register/manual_register
fi
# Run SAW register
## Stitch microscope tile images to a panoramic image, perform tissue and cell (optional, depends on -doCellBin) segmentation, and register the panoramic image and the segmentated images with the gene expression matrix
geneExp=$dataDir/02.count/${SN}.raw.gef
if [[ -f $imageTarFile ]] && [[ -f $iprFile ]] && [[ $doCell == "Y" ]]; then
## Run SAW register (stitch, tissue segmentation, cell segmentation) + SAW imageTools
echo `date` "=> image processing and registration start......."
export HDF5_USE_FILE_LOCKING=FALSE
imgTarDIR=$(dirname $imageTarFile)
iprDIR=$(dirname $iprFile)
export SINGULARITY_BIND=$outDir,$imgTarDIR,$iprDIR,$dataDir
cp -rf ${iprFile} ${result_03register}/${SN}.reregist.ipr
/usr/bin/time -v singularity exec ${sif} manualRegister \
-i ${tifDir} \
-c ${result_03register}/${SN}.reregist.ipr \
-v ${geneExp} \
-f $flip \
-r $rotate \
-o $offsetX $offsetY \
-s $extrude_x $extrude_y \
-a $isTuned \
-p ${result_03register}
out_iprFile=$(find ${result_03register} -maxdepth 1 -name \*.ipr | head -1)
/usr/bin/time -v singularity exec ${sif} imageTools ipr2img \
-i ${imageTarFile} \
-c ${out_iprFile} \
-d tissue cell \
-r True \
-o ${result_03register}
elif [[ -f $imageTarFile ]] && [[ -f $iprFile ]] && [[ $doCell == "N" ]]; then
# Run SAW rapidRegister (stitch, tissue segmentation) + SAW imageTools
echo `date` "=> image processing and registration start......."
export HDF5_USE_FILE_LOCKING=FALSE
imgTarDIR=$(dirname $imageTarFile)
iprDIR=$(dirname $iprFile)
export SINGULARITY_BIND=$outDir,$imgTarDIR,$iprDIR,$dataDir
cp -rf ${iprFile} ${result_03register}/${SN}.reregist.ipr
/usr/bin/time -v singularity exec ${sif} manualRegister \
-i ${tifDir} \
-c ${result_03register}/${SN}.reregist.ipr \
-v ${geneExp} \
-f $flip \
-r $rotate \
-o $offsetX $offsetY \
-s $extrude_x $extrude_y \
-a $isTuned \
-p ${result_03register}
out_iprFile=$(find ${result_03register} -maxdepth 1 -name \*.ipr | head -1)
/usr/bin/time -v singularity exec ${sif} imageTools ipr2img \
-i ${imageTarFile} \
-c $out_iprFile \
-d tissue \
-r True \
-o ${result_03register}
fi
# Run SAW tissueCut
echo `date` "=> tissueCut start......."
if [[ -f $imageTarFile ]] && [[ -f $iprFile ]]; then
## Run tissueCut to get the spatial gene expression profile of the tissue-covered region
transformedTif=$(find ${result_03register} -maxdepth 1 -name \*fov_stitched_transformed.tif)
if [[ -n $transformedTif ]]
then
nucleusLayer=$(find ${result_03register} -maxdepth 1 -name \*fov_stitched_transformed.tif -exec sh -c 'for f do basename -- "$f" _fov_stitched_transformed.tif;done' sh {} + | grep -v IF | awk -F_ '{print$1}')
else
nucleusLayer=$(find ${result_03register} -maxdepth 1 -name \*fov_stitched.tif -exec sh -c 'for f do basename -- "$f" _fov_stitched.tif;done' sh {} + | grep -v IF | awk -F_ '{print$1}')
fi
tissueMaskFile=$(find ${result_03register} -maxdepth 1 -name ${nucleusLayer}_${SN}_tissue_cut.tif)
export HDF5_USE_FILE_LOCKING=FALSE
export SINGULARITY_BIND=$outDir,$dataDir
/usr/bin/time -v singularity exec ${sif} tissueCut \
-i ${geneExp} \
--dnbfile ${barcodeReadsCounts} \
-s ${tissueMaskFile} \
--sn ${SN} \
-O Transcriptomics \
-d -t 8 \
-o ${result_04tissuecut}
/usr/bin/time -v singularity exec ${sif} cellCut bgef \
-i ${result_04tissuecut}/${SN}.tissue.gef \
-o ${result_04tissuecut}/${SN}.${nucleusLayer}.gef \
-O Transcriptomics \
-b 1,5,10,20,50,100,150,200
for i in `singularity exec ${sif} h5dump -n ${result_03register}/${SN}.reregist.ipr | grep 'Labeling/' | grep -v 'Labeling/.*/Canvas'|grep -v 'Labeling/.*/Element'|awk '{print$2}'`;
do
label=`basename $i`
mkdir -p ${result_04tissuecut}/tissuecut_${label}
labelmask=$(find ${result_03register} -name \*${label}_tissue_cut.tif)
echo $labelmask
/usr/bin/time -v singularity exec ${sif} tissueCut \
-l $label \
-i ${geneExp} \
--dnbfile ${barcodeReadsCounts} \
-s ${labelmask} \
--sn ${SN} \
-O Transcriptomics \
-d -t 8 \
-o ${result_04tissuecut}/tissuecut_${label}
done
else
## Run SAW tissueCut based on the gene expression matrix directly
export SINGULARITY_BIND=$outDir,$refDIR,$dataDir
echo `date` "=> there is no image, tissueCut based on the gene expression matrix start......."
export HDF5_USE_FILE_LOCKING=FALSE
/usr/bin/time -v singularity exec ${sif} tissueCut \
-i ${geneExp} \
--dnbfile ${barcodeReadsCounts} \
--sn ${SN} \
-O Transcriptomics \
-d -t 8 \
-o ${result_04tissuecut}
fi
# Complete raw GEF to visual GEF
export HDF5_USE_FILE_LOCKING=FALSE
/usr/bin/time -v singularity exec ${sif} cellCut bgef \
-i ${geneExp} \
-o ${result_04tissuecut}/${SN}.gef \
-O Transcriptomics
# Complete raw labeled tissue GEF to visual GEF
if [[ -f $imageTarFile ]] && [[ -f $iprFile ]]; then
for i in `singularity exec ${sif} h5dump -n ${result_03register}/${SN}.reregist.ipr | grep 'Labeling/' | grep -v 'Labeling/.*/Canvas'|grep -v 'Labeling/.*/Element'|awk '{print$2}'`;
do
label=`basename $i`
export HDF5_USE_FILE_LOCKING=FALSE
/usr/bin/time -v singularity exec ${sif} cellCut bgef \
-i ${result_04tissuecut}/tissuecut_${label}/${SN}.${label}.raw.label.gef \
-o ${result_04tissuecut}/tissuecut_${label}/${SN}.${label}.label.gef \
-O Transcriptomics
done
fi
## Convert GEF to GEM [optional]
/usr/bin/time -v singularity exec ${sif} cellCut view \
-s ${SN} \
-i ${result_04tissuecut}/${SN}.gef \
-o ${result_04tissuecut}/${SN}.gem
gzip ${result_04tissuecut}/${SN}.gem
/usr/bin/time -v singularity exec ${sif} cellCut view \
-s ${SN} \
-i ${result_04tissuecut}/${SN}.tissue.gef \
-o ${result_04tissuecut}/${SN}.tissue.gem
gzip ${result_04tissuecut}/${SN}.tissue.gem
# Run spatialCluster
export SINGULARITY_BIND=$outDir,$dataDir
echo `date` "=> spatialCluster start......."
export HDF5_USE_FILE_LOCKING=FALSE
mkdir -p ${outDir}/tmp
export NUMBA_CACHE_DIR=${outDir}/tmp
export MPLCONFIGDIR=${outDir}/tmp
binSize=200
resolution=1.0
/usr/bin/time -v singularity exec ${sif} spatialCluster \
-i ${result_04tissuecut}/${SN}.tissue.gef \
-o ${result_05spatialcluster}/${SN}.bin${binSize}_${resolution}.spatial.cluster.h5ad \
-s ${binSize} \
-r ${resolution}
## output labeled spatial H5AD [optional]
#for i in `singularity exec ${sif} h5dump -n ${result_03register}/${SN}.reregist.ipr | grep 'Labeling/' | grep -v 'Labeling/.*/Canvas'|grep -v 'Labeling/.*/Element'|awk '{print$2}'`;
#do
#label=`basename $i`
#echo $labelmask
#export HDF5_USE_FILE_LOCKING=FALSE
#/usr/bin/time -v singularity exec ${sif} spatialCluster \
# -i ${outDir}/04.tissuecut/tissuecut_${label}/${SN}.${label}.label.gef \
# -s ${binSize} \
# -r ${resolution} \
# -o ${outDir}/05.spatialcluster/${SN}.${label}.bin${binSize}_${resolution}.spatial.cluster.h5ad
#done
# Run cellCut, cellCorrect, cellCluster and cellChunk
export SINGULARITY_BIND=$outDir,$dataDir
if [[ -f $imageTarFile ]] && [[ -f $iprFile ]] && [[ $doCell == "Y" ]]; then
## Run SAW cellCut
echo `date` "=> cellCut start......."
export HDF5_USE_FILE_LOCKING=FALSE
transformedTif=$(find ${outDir}/03.register -maxdepth 1 -name \*fov_stitched_transformed.tif)
if [[ -n $transformedTif ]]
then
nucleusLayer=$(find ${outDir}/03.register -maxdepth 1 -name \*fov_stitched_transformed.tif -exec sh -c 'for f do basename -- "$f" _fov_stitched_transformed.tif;done' sh {} + | grep -v IF | awk -F_ '{print$1}')
else
nucleusLayer=$(find ${outDir}/03.register -maxdepth 1 -name \*fov_stitched.tif -exec sh -c 'for f do basename -- "$f" _fov_stitched.tif;done' sh {} + | grep -v IF | awk -F_ '{print$1}')
fi
nucleusMask=$(find ${outDir}/03.register -maxdepth 1 -name ${nucleusLayer}_${SN}_mask.tif)
/usr/bin/time -v singularity exec ${sif} cellCut cgef \
-i ${geneExp} \
-m ${nucleusMask} \
-o ${result_041cellcut}/${SN}.cellbin.gef
## Run SAW cellCorrect
echo `date` "=> cellCorrect start......."
export HDF5_USE_FILE_LOCKING=FALSE
/usr/bin/time -v singularity exec ${sif} cellCorrect \
-i ${dataDir}/02.count/${SN}.raw.gef \
-m ${nucleusMask} \
-d 10 \
-o ${result_041cellcut}
## Write the adjusted mask image into SN.rpi
cellCorrectMask=$(find ${result_041cellcut} -maxdepth 1 -name ${nucleusLayer}_${SN}_mask_edm_dis\*.tif)
/usr/bin/time -v singularity exec ${sif} imageTools img2rpi \
-i ${cellCorrectMask} \
-g ${nucleusLayer}/CellMask_adjusted \
-b 2 10 50 100 150 \
-o ${result_03register}/${SN}.rpi
## Run SAW cellCluster
echo `date` "=> cellCluster start......."
mkdir -p ${outDir}/tmp
export NUMBA_CACHE_DIR=${outDir}/tmp
export MPLCONFIGDIR=${outDir}/tmp
/usr/bin/time -v singularity exec ${sif} cellCluster \
-i ${outDir}/041.cellcut/${SN}.adjusted.cellbin.gef \
-o ${outDir}/051.cellcluster/${SN}.adjusted.cell.cluster.h5ad
/usr/bin/time -v singularity exec ${sif} cellCluster \
-i ${outDir}/041.cellcut/${SN}.cellbin.gef \
-o ${outDir}/051.cellcluster/${SN}.cell.cluster.h5ad
## Run SAW cellChunk to write rendering data into cellbin.gef
echo `date` "=> cellChunk start......."
/usr/bin/time -v singularity exec ${sif} cellChunk \
-i ${result_041cellcut}/${SN}.adjusted.cellbin.gef \
-o ${result_041cellcut}
/usr/bin/time -v singularity exec ${sif} cellChunk \
-i ${result_041cellcut}/${SN}.cellbin.gef \
-o ${result_041cellcut}
fi
# Run saturation
export SINGULARITY_BIND=$outDir,$dataDir
echo `date` "=> saturation start ......"
export HDF5_USE_FILE_LOCKING=FALSE
saturationFile=${dataDir}/02.count/${SN}_raw_barcode_gene_exp.txt
/usr/bin/time -v singularity exec ${sif} saturation \
-i ${saturationFile} \
--tissue ${result_04tissuecut}/${SN}.tissue.gef \
-o ${result_06saturation} \
--bcstat ${bcStatStr} \
--summary ${dataDir}/02.count/${SN}.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat
# Run report to generate HTML report
echo `date` "=> report generation start......"
export HDF5_USE_FILE_LOCKING=FALSE
export SINGULARITY_BIND=$outDir,$dataDir
out_iprFile=$(find ${result_03register} -maxdepth 1 -name \*.ipr | head -1)
pipever=$(basename ${sif} .sif)
if [[ -n ${out_iprFile} ]] && [[ -e ${out_iprFile} ]] && [[ $doCell == 'Y' ]]; then
/usr/bin/time -v singularity exec ${sif} report \
-m ${bcStatStr} \
-a ${bcFinalOutStr} \
-g ${dataDir}/02.count/${SN}.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat \
-l ${result_04tissuecut}/tissuecut.stat \
-n ${result_04tissuecut}/${SN}.gef \
-i ${result_03register}/${SN}.rpi \
-d ${result_05spatialcluster}/${SN}.bin${binSize}_${resolution}.spatial.cluster.h5ad \
-t ${result_06saturation}/plot_200x200_saturation.png \
-b ${result_04tissuecut}/tissue_fig/scatter_200x200_MID_gene_counts.png \
-v ${result_04tissuecut}/tissue_fig/violin_200x200_MID_gene.png \
-c ${result_04tissuecut}/tissue_fig/statistic_200x200_MID_gene_DNB.png \
--bin20Saturation ${result_04tissuecut}/tissue_fig/scatter_20x20_MID_gene_counts.png \
--bin20violin ${result_04tissuecut}/tissue_fig/violin_20x20_MID_gene.png \
--bin20MIDGeneDNB ${result_04tissuecut}/tissue_fig/statistic_20x20_MID_gene_DNB.png \
--bin50Saturation ${result_04tissuecut}/tissue_fig/scatter_50x50_MID_gene_counts.png \
--bin50violin ${result_04tissuecut}/tissue_fig/violin_50x50_MID_gene.png \
--bin50MIDGeneDNB ${result_04tissuecut}/tissue_fig/statistic_50x50_MID_gene_DNB.png \
--bin100Saturation ${result_04tissuecut}/tissue_fig/scatter_100x100_MID_gene_counts.png \
--bin100violin ${result_04tissuecut}/tissue_fig/violin_100x100_MID_gene.png \
--bin100MIDGeneDNB ${result_04tissuecut}/tissue_fig/statistic_100x100_MID_gene_DNB.png \
--bin150Saturation ${result_04tissuecut}/tissue_fig/scatter_150x150_MID_gene_counts.png \
--bin150violin ${result_04tissuecut}/tissue_fig/violin_150x150_MID_gene.png \
--bin150MIDGeneDNB ${result_04tissuecut}/tissue_fig/statistic_150x150_MID_gene_DNB.png \
--cellBinGef ${result_041cellcut}/${SN}.adjusted.cellbin.gef \
--cellCluster ${result_051cellcluster}/${SN}.adjusted.cell.cluster.h5ad \
--iprFile ${out_iprFile} \
--pipelineVersion ${pipever} \
-s ${SN} \
--species ${refName} \
--tissue ${tissueType} \
--reference ${refName} \
-o ${result_07report}
elif [[ -n ${out_iprFile} ]] && [[ -e ${out_iprFile} ]] && [[ $doCell == 'N' ]]; then
/usr/bin/time -v singularity exec ${sif} report \
-m ${bcStatStr} \
-a ${bcFinalOutStr} \
-g ${dataDir}/02.count/${SN}.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat \
-l ${result_04tissuecut}/tissuecut.stat \
-n ${result_04tissuecut}/${SN}.gef \
-i ${result_03register}/${SN}.rpi \
-d ${result_05spatialcluster}/${SN}.bin${binSize}_${resolution}.spatial.cluster.h5ad \
-t ${result_06saturation}/plot_200x200_saturation.png \
-b ${result_04tissuecut}/tissue_fig/scatter_200x200_MID_gene_counts.png \
-v ${result_04tissuecut}/tissue_fig/violin_200x200_MID_gene.png \
-c ${result_04tissuecut}/tissue_fig/statistic_200x200_MID_gene_DNB.png \
--bin20Saturation ${result_04tissuecut}/tissue_fig/scatter_20x20_MID_gene_counts.png \
--bin20violin ${result_04tissuecut}/tissue_fig/violin_20x20_MID_gene.png \
--bin20MIDGeneDNB ${result_04tissuecut}/tissue_fig/statistic_20x20_MID_gene_DNB.png \
--bin50Saturation ${result_04tissuecut}/tissue_fig/scatter_50x50_MID_gene_counts.png \
--bin50violin ${result_04tissuecut}/tissue_fig/violin_50x50_MID_gene.png \
--bin50MIDGeneDNB ${result_04tissuecut}/tissue_fig/statistic_50x50_MID_gene_DNB.png \
--bin100Saturation ${result_04tissuecut}/tissue_fig/scatter_100x100_MID_gene_counts.png \
--bin100violin ${result_04tissuecut}/tissue_fig/violin_100x100_MID_gene.png \
--bin100MIDGeneDNB ${result_04tissuecut}/tissue_fig/statistic_100x100_MID_gene_DNB.png \
--bin150Saturation ${result_04tissuecut}/tissue_fig/scatter_150x150_MID_gene_counts.png \
--bin150violin ${result_04tissuecut}/tissue_fig/violin_150x150_MID_gene.png \
--bin150MIDGeneDNB ${result_04tissuecut}/tissue_fig/statistic_150x150_MID_gene_DNB.png \
--iprFile ${out_iprFile} \
--pipelineVersion ${pipever} \
-s ${SN} \
--species ${refName} \
--tissue ${tissueType} \
--reference ${refName} \
-o ${result_07report}
else
/usr/bin/time -v singularity exec ${sif} report \
-m ${bcStatStr} \
-a ${bcFinalOutStr} \
-g ${dataDir}/02.count/${SN}.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat \
-l ${result_04tissuecut}/tissuecut.stat \
-n ${result_04tissuecut}/${SN}.gef \
-d ${result_05spatialcluster}/${SN}.bin${binSize}_${resolution}.spatial.cluster.h5ad \
-t ${result_06saturation}/plot_200x200_saturation.png \
-b ${result_04tissuecut}/tissue_fig/scatter_200x200_MID_gene_counts.png \
-v ${result_04tissuecut}/tissue_fig/violin_200x200_MID_gene.png \
-c ${result_04tissuecut}/tissue_fig/statistic_200x200_MID_gene_DNB.png \
--bin20Saturation ${result_04tissuecut}/tissue_fig/scatter_20x20_MID_gene_counts.png \
--bin20violin ${result_04tissuecut}/tissue_fig/violin_20x20_MID_gene.png \
--bin20MIDGeneDNB ${result_04tissuecut}/tissue_fig/statistic_20x20_MID_gene_DNB.png \
--bin50Saturation ${result_04tissuecut}/tissue_fig/scatter_50x50_MID_gene_counts.png \
--bin50violin ${result_04tissuecut}/tissue_fig/violin_50x50_MID_gene.png \
--bin50MIDGeneDNB ${result_04tissuecut}/tissue_fig/statistic_50x50_MID_gene_DNB.png \
--bin100Saturation ${result_04tissuecut}/tissue_fig/scatter_100x100_MID_gene_counts.png \
--bin100violin ${result_04tissuecut}/tissue_fig/violin_100x100_MID_gene.png \
--bin100MIDGeneDNB ${result_04tissuecut}/tissue_fig/statistic_100x100_MID_gene_DNB.png \
--bin150Saturation ${result_04tissuecut}/tissue_fig/scatter_150x150_MID_gene_counts.png \
--bin150violin ${result_04tissuecut}/tissue_fig/violin_150x150_MID_gene.png \
--bin150MIDGeneDNB ${result_04tissuecut}/tissue_fig/statistic_150x150_MID_gene_DNB.png \
--pipelineVersion ${pipever} \
-s ${SN} \
--species ${refName} \
--tissue ${tissueType} \
--reference ${refName} \
-o ${result_07report}
fi
# Organize files required by StereoMap
## 03.register
if [[ -f $result_03register/${SN}.rpi ]] || [[ -f out_iprFile ]]
then
ln -s $result_03register/${SN}.rpi $result_visualization/${SN}.rpi
ln -s $out_iprFile $result_visualization/$(basename "$out_iprFile")
fi
## 04.tissuecut
if [[ -f $result_04tissuecut/${SN}.gef ]]
then
ln -s $result_04tissuecut/${SN}.gef $result_visualization/${SN}.gef
fi
for i in `singularity exec ${sif} h5dump -n ${result_03register}/${SN}.reregist.ipr | grep 'Labeling/' | grep -v 'Labeling/.*/Canvas'|grep -v 'Labeling/.*/Element'|awk '{print$2}'`;
do
label=`basename $i`
if [[ -f $result_04tissuecut/tissuecut_${label}/${SN}.${label}.label.gef ]]
then
ln -s $result_04tissuecut/tissuecut_${label}/${SN}.${label}.label.gef $result_visualization/${SN}.${label}.label.gef
fi
done
## 041.cellcut
if [[ -f $result_041cellcut/${SN}.adjusted.cellbin.gef ]]
then
ln -s $result_041cellcut/${SN}.adjusted.cellbin.gef $result_visualization/${SN}.adjusted.cellbin.gef
fi
## 05.spatialCluster
if [[ -f $result_05spatialcluster/${SN}.bin${binSize}_${resolution}.spatial.cluster.h5ad ]]
then
ln -s $result_05spatialcluster/${SN}.bin${binSize}_${resolution}.spatial.cluster.h5ad $result_visualization/${SN}.bin${binSize}_${resolution}.spatial.cluster.h5ad
fi
#for i in `singularity exec ${sif} h5dump -n ${result_03register}/${SN}.reregist.ipr | grep 'Labeling/' | grep -v 'Labeling/.*/Canvas'|grep -v 'Labeling/.*/Element'|awk '{print$2}'`;
#do
#label=`basename $i`
# if [[ -f $result_05spatialcluster/${SN}.${label}.bin${binSize}_${resolution}.spatial.cluster.h5ad ]]
# then
# ln -s $result_05spatialcluster/${SN}.${label}.bin${binSize}_${resolution}.spatial.cluster.h5ad $result_visualization/${SN}.${label}.bin${binSize}_${resolution}.spatial.cluster.h5ad
# fi
#done
## 051.cellCluster
if [[ -f $result_051cellcluster/${SN}.cell.cluster.h5ad ]]
then
ln -s $result_051cellcluster/${SN}.cell.cluster.h5ad $result_visualization/${SN}.cell.cluster.h5ad
fi
echo `date` " All done! "