add multi-file version

broadinstitute · Dec 12, 2023 · 4708cec · 4708cec
1 parent 5e64745
commit 4708cec
Showing 1 changed file with 17 additions and 0 deletions.
diff --git a/scripts/mcp_and_decompress.sh b/scripts/mcp_and_decompress.sh
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+INFILES=${@:1:$#-1}
+OUTDIR=${@:$#}
+
+for INFILE in $INFILES; do
+    if [[ $INFILE == *.gz ]]; then
+        OUTFNAME=$(basename $INFILE .gz)
+        pigz -dc $INFILE > "$OUTDIR/$OUTFNAME"
+    elif [[ $INFILE == *.zst ]]; then
+        OUTFNAME=$(basename $INFILE .zst)
+        zstd -d $INFILE -o "$OUTDIR/$OUTFNAME"
+    else
+        OUTFNAME=$(basename $INFILE)
+        cp $INFILE "$OUTDIR/$OUTFNAME"
+    fi
+done