remove module_dir variable

analyses/cell-type-consensus/assign-consensus-celltypes.sh

@@ -11,21 +11,18 @@ set -euo pipefail
 
 # navigate to where script lives
 cd $(dirname "$0")
-module_dir=$(pwd)
+#module_dir=$(pwd)
 
-data_dir="${module_dir}/../../data/current"
+data_dir="../../data/current"
 # path to save consensus results 
-scpca_consensus_assignments_file="${module_dir}/results/scpca-consensus-celltype-assignments.tsv"
+scpca_consensus_assignments_file="results/scpca-consensus-celltype-assignments.tsv"
 # directory to store all individual tsv files 
-celltype_tsv_dir="${module_dir}/results/original-celltype-assignments" 
+celltype_tsv_dir="results/original-celltype-assignments" 
 mkdir -p ${celltype_tsv_dir}
 
-# define scripts and notebook directories
-scripts_dir="${module_dir}/scripts"
-
 # define reference input files 
-panglao_ref_file="${module_dir}/references/panglao-cell-type-ontologies.tsv"
-consensus_ref_file="${module_dir}/references/consensus-cell-type-reference.tsv"
+panglao_ref_file="references/panglao-cell-type-ontologies.tsv"
+consensus_ref_file="references/consensus-cell-type-reference.tsv"
 
 # run script to export tsv file on all processed objects
 for sce_file in $data_dir/*/SCPCS*/*_processed.rds; do
@@ -35,15 +32,15 @@ for sce_file in $data_dir/*/SCPCS*/*_processed.rds; do
 
     echo "Grabbing cell types for ${library_id}"
     # get celltypes as tsv file 
-    Rscript $scripts_dir/03-save-coldata.R \
+    Rscript scripts/03-save-coldata.R \
       --sce_file $sce_file \
       --output_file ${celltype_tsv_dir}/${library_id}_celltype-assignments.tsv
 
 done 
 
 echo "Combining TSVs and adding consensus labels"
 # run script to combine all tsv files and assign consensus cell types
-Rscript $scripts_dir/04-combine-celltype-tables.R \
+Rscript scripts/04-combine-celltype-tables.R \
   --celltype_tsv_dir $celltype_tsv_dir \
   --panglao_ref_file $panglao_ref_file \
   --consensus_ref_file $consensus_ref_file \