From e3d05c9f48cd31ebce7481b96f98b77aa716e962 Mon Sep 17 00:00:00 2001
From: wbaopaul <yuw1@email.chop.edu>
Date: Fri, 29 Apr 2022 13:59:15 -0400
Subject: [PATCH] minor update after release

---
 scripts/integrate_mtx.sh  |  2 +-
 scripts/integrate_peak.sh | 23 +++++++++++++++++++++++
 2 files changed, 24 insertions(+), 1 deletion(-)

diff --git a/scripts/integrate_mtx.sh b/scripts/integrate_mtx.sh
index 37754b6..dbbcb63 100755
--- a/scripts/integrate_mtx.sh
+++ b/scripts/integrate_mtx.sh
@@ -24,7 +24,7 @@ if [ "$prepCello4Integration" = "TRUE" ]; then
     if [[ $Integrate_By == "seurat"  ]]; then
         assay4cello=integrated
     fi
-    ${R_PATH}/Rscript --vanilla ${curr_dir}/src/interface2cello.R $seurat_file $assay4cello
+    ${R_PATH}/Rscript --vanilla ${curr_dir}/src/interface2cello.R $seurat_file $assay4cello $TSS
     ## write config file
     organism=hsa
     if [[ $GENOME_NAME =~ "mm" ]]; then
diff --git a/scripts/integrate_peak.sh b/scripts/integrate_peak.sh
index f355d98..c973f7a 100755
--- a/scripts/integrate_peak.sh
+++ b/scripts/integrate_peak.sh
@@ -64,3 +64,26 @@ mtx_files=${mtx_files/TMP,/}
 
 ${R_PATH}/Rscript --vanilla ${curr_dir}/src/integrate_mtx.R $mtx_files $K_CLUSTERS $integrated_dir $GENOME_NAME $TSS $norm_by $REDUCTION $nREDUCTION $Top_Variable_Features $Integrate_By
 
+abs_out_dir=`cd ${integrated_dir}; pwd`
+
+if [ "$prepCello4Integration" = "TRUE" ]; then
+    seurat_file=${abs_out_dir}/seurat_obj_${Integrate_By}.rds
+    assay4cello=ATAC
+    if [[ $Integrate_By == "seurat"  ]]; then
+        assay4cello=integrated
+    fi
+    ${R_PATH}/Rscript --vanilla ${curr_dir}/src/interface2cello.R $seurat_file $assay4cello $TSS
+    ## write config file
+    organism=hsa
+    if [[ $GENOME_NAME =~ "mm" ]]; then
+        organism=mmu
+    fi
+
+    echo "default:" > ${abs_out_dir}/VisCello_obj/config.yml
+    echo "  study_name: $OUTPUT_PREFIX_integrated " >> ${abs_out_dir}/VisCello_obj/config.yml
+    echo "  study_description: NNN " >> ${abs_out_dir}/VisCello_obj/config.yml
+    echo "  organism: $organism " >> ${abs_out_dir}/VisCello_obj/config.yml
+    echo "  feature_name_column: 'symbol' " >> ${abs_out_dir}/VisCello_obj/config.yml
+    echo "  feature_id_column: 'symbol' " >> ${abs_out_dir}/VisCello_obj/config.yml
+fi
+