Minor changes, paths, config and script

emmarousseau · Apr 11, 2024 · 166de17 · 166de17
1 parent 72fd99f
commit 166de17
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/src/samtools/samtools_stats/config.vsh.yaml b/src/samtools/samtools_stats/config.vsh.yaml
@@ -143,7 +143,7 @@ argument_groups:
         Output file.
       default: "out.txt"
       required: true
-      must_exist: false
+      direction: output
 
 resources:
   - type: bash_script

diff --git a/src/samtools/samtools_stats/script.sh b/src/samtools/samtools_stats/script.sh
@@ -10,7 +10,7 @@ set -e
 [[ "$par_sparse" == "false" ]] && unset par_sparse
 [[ "$par_remove_overlaps" == "false" ]] && unset par_remove_overlaps
 
-$(which samtools) stats \
+samtools stats \
     ${par_coverage:+-c "$par_coverage"} \
     ${par_remove_dups:+-d} \
     ${par_required_flag:+-f "$par_required_flag"} \

diff --git a/src/samtools/samtools_stats/test.sh b/src/samtools/samtools_stats/test.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-test_dir="${meta_resources_dir}test_data"
+test_dir="${meta_resources_dir}/test_data"
 
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