Built on 2024-02-20, v0.1.53.3

neurobioinfo · Feb 20, 2024 · 55a2092 · 55a2092
1 parent e3ae1fe
commit 55a2092
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Showing 10 changed files with 11 additions and 11 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/scrnabox.pip/.DS_Store b/scrnabox.pip/.DS_Store
diff --git a/scrnabox.pip/hto/.DS_Store b/scrnabox.pip/hto/.DS_Store
diff --git a/scrnabox.pip/hto/pars/step1_par.txt b/scrnabox.pip/hto/pars/step1_par.txt
@@ -49,7 +49,7 @@ par_automated_library_prep= "no"
 # CellRanger counts pipeline parameters.
 ##################################################################################
 ## Path to reference genome
-par_ref_dir='/path/to/CellRanger/reference/genome'
+par_ref_dir_grch='/path/to/CellRanger/reference/genome'
 
 ## Minimum number of bases to retain for R1 sequence of gene expression assay. If you want to use this parameter uncomment the line below and define your par_r1_length.
 #par_r1_length=20

diff --git a/scrnabox.pip/hto/scripts/.DS_Store b/scrnabox.pip/hto/scripts/.DS_Store
diff --git a/scrnabox.pip/hto/scripts/step1/create_cellranger_hto.sh b/scrnabox.pip/hto/scripts/step1/create_cellranger_hto.sh
@@ -74,10 +74,10 @@ cellranger count \\
     --jobmode=\${SLURM_TEMPLATE} \\
 EOF
 
-# par_ref_dir
-if [[ -n "${par_ref_dir}" ]]; then
+# par_ref_dir_grch
+if [[ -n "${par_ref_dir_grch}" ]]; then
 cat <<EOF >> $OUTFILE
-    --transcriptome=\${par_ref_dir} \\
+    --transcriptome=\${par_ref_dir_grch} \\
 EOF
 fi
 

diff --git a/scrnabox.pip/hto/scripts/step1/create_cellranger_hto_local.sh b/scrnabox.pip/hto/scripts/step1/create_cellranger_hto_local.sh
@@ -72,9 +72,9 @@ cellranger count \\
 EOF
 
 # par_ref_dir
-if [[ -n "${par_ref_dir}" ]]; then
+if [[ -n "${par_ref_dir_grch}" ]]; then
 cat <<EOF >> $OUTFILE
-    --transcriptome=\${par_ref_dir} \\
+    --transcriptome=\${par_ref_dir_grch} \\
 EOF
 fi
 

diff --git a/scrnabox.pip/scrna/pars/step1_par.txt b/scrnabox.pip/scrna/pars/step1_par.txt
@@ -27,7 +27,7 @@ par_automated_library_prep= "no"
 # CellRanger counts pipeline parameters.
 ##################################################################################
 ## Path to reference genome
-par_ref_dir='/path/to/CellRanger/reference/genome'
+par_ref_dir_grch='/path/to/CellRanger/reference/genome'
 
 ## Minimum number of bases to retain for R1 sequence of gene expression assay. If you want to use this parameter uncomment the line below and define your par_r1_length.
 #par_r1_length=20

diff --git a/scrnabox.pip/scrna/scripts/step1/create_cellranger_scrna.sh b/scrnabox.pip/scrna/scripts/step1/create_cellranger_scrna.sh
@@ -74,10 +74,10 @@ cellranger count \\
     --jobmode=\${SLURM_TEMPLATE} \\
 EOF
 
-# par_ref_dir
-if [[ -n "${par_ref_dir}" ]]; then
+# par_ref_dir_grch
+if [[ -n "${par_ref_dir_grch}" ]]; then
 cat <<EOF >> $OUTFILE
-    --transcriptome=\${par_ref_dir} \\
+    --transcriptome=\${par_ref_dir_grch} \\
 EOF
 fi
 

diff --git a/scrnabox.pip/scrna/scripts/step1/create_cellranger_scrna_local.sh b/scrnabox.pip/scrna/scripts/step1/create_cellranger_scrna_local.sh
@@ -72,7 +72,7 @@ cellranger count \\
     --libraries=\${LIBRARY} \\
 EOF
 
-# par_ref_dir
+# par_ref_dir_grch
 if [[ -n "${par_ref_dir_grch}" ]]; then
 cat <<EOF >> $OUTFILE
     --transcriptome=\${par_ref_dir_grch} \\