adding n_score option

src/bedtools/bedtools_bed12tobed6/config.vsh.yaml

@@ -37,7 +37,7 @@ argument_groups:
 
   - name: Options
     arguments:
-      - name: --n
+      - name: --n_score
         alternatives: -n
         type: boolean_true
         description: | 
@@ -63,4 +63,5 @@ engines:
 
 runners:
   - type: executable
-  - type: nextflow
+  - type: nextflow
+

src/bedtools/bedtools_bed12tobed6/script.sh

@@ -5,7 +5,11 @@
 
 set -eo pipefail
 
+# Unset parameters
+[[ "$par_n_score" == "false" ]] && unset par_n_score
+
 # Execute bedtools bed12tobed6 conversion 
 bedtools bed12tobed6 \
+    ${par_n_score:+-n} \
     -i "$par_input" \
     > "$par_output"

src/bedtools/bedtools_bed12tobed6/test.sh

@@ -41,6 +41,12 @@ chr21	10079666	10120808	uc002yiv.1	0	-
 chr21	10080031	10081687	uc002yiw.1	0	-
 chr21	10081660	10120796	uc002yix.2	0	-
 EOF
+# Expected output bed6 file
+cat <<EOF > "$TMPDIR/expected_n.bed6"
+chr21	10079666	10120808	uc002yiv.1	1	-
+chr21	10080031	10081687	uc002yiw.1	1	-
+chr21	10081660	10120796	uc002yix.2	1	-
+EOF
 
 # Test 1: Default conversion BED12 to BED6
 mkdir "$TMPDIR/test1" && pushd "$TMPDIR/test1" > /dev/null
@@ -58,5 +64,22 @@ echo "- test1 succeeded -"
 
 popd > /dev/null
 
+# Test 2: Conversion BED12 to BED6 with -n option
+mkdir "$TMPDIR/test2" && pushd "$TMPDIR/test2" > /dev/null
+
+echo "> Run bedtools_bed12tobed6 on BED12 file with -n option"
+"$meta_executable" \
+  --input "../example.bed12" \
+  --output "output.bed6" \
+  --n_score
+
+# checks
+assert_file_exists "output.bed6"
+assert_file_not_empty "output.bed6"
+assert_identical_content "output.bed6" "../expected_n.bed6"
+echo "- test2 succeeded -"
+
+popd > /dev/null
+
 echo "---- All tests succeeded! ----"
 exit 0