compress output

AlexsLemonade · Jan 9, 2025 · bcb16a5 · bcb16a5
1 parent 939103f
commit bcb16a5
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/analyses/cell-type-consensus/assign-consensus-celltypes.sh b/analyses/cell-type-consensus/assign-consensus-celltypes.sh
@@ -15,7 +15,7 @@ cd $(dirname "$0")
 
 data_dir="../../data/current"
 # path to save consensus results 
-scpca_consensus_assignments_file="results/scpca-consensus-celltype-assignments.tsv"
+scpca_consensus_assignments_file="results/scpca-consensus-celltype-assignments.tsv.gz"
 # directory to store all individual tsv files 
 celltype_tsv_dir="results/original-celltype-assignments" 
 mkdir -p ${celltype_tsv_dir}

diff --git a/analyses/cell-type-consensus/scripts/04-combine-celltype-tables.R b/analyses/cell-type-consensus/scripts/04-combine-celltype-tables.R
@@ -34,7 +34,8 @@ option_list <- list(
   make_option(
     opt_str = c("--output_file"),
     type = "character",
-    help = "Path to file where combined TSV file will be saved, must end in `.tsv`"
+    help = "Path to file where combined TSV file will be saved. 
+      File name must end in either `.tsv` or `.tsv.gz` to save a compressed TSV file"
   )
 )
 
@@ -46,7 +47,8 @@ opt <- parse_args(OptionParser(option_list = option_list))
 # make sure reference files exist 
 stopifnot(
   "panglao reference file does not exist" = file.exists(opt$panglao_ref_file),
-  "cell type consensus reference file does not exist" = file.exists(opt$consensus_ref_file)
+  "cell type consensus reference file does not exist" = file.exists(opt$consensus_ref_file),
+  "output file must end in `.tsv` or `.tsv.gz`" = stringr::str_detect(opt$output_file, ".tsv|.tsv.gz")
 )
 
 # read in ref files