Minor changes, paths, config and script

emmarousseau · Apr 11, 2024 · f25ca06 · f25ca06
1 parent 576d926
commit f25ca06
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/src/samtools/samtools_sort/config.vsh.yaml b/src/samtools/samtools_sort/config.vsh.yaml
@@ -25,7 +25,7 @@ argument_groups:
         description: |
           Write final output to file.
         required: true
-        must_exist: false
+        direction: output
         example: out.bam
       - name: --output_fmt
         alternatives: -O

diff --git a/src/samtools/samtools_sort/script.sh b/src/samtools/samtools_sort/script.sh
@@ -16,7 +16,7 @@ set -e
 [[ "$par_no_PG" == "false" ]] && unset par_no_PG
 
 
-$(which samtools) sort \
+samtools sort \
     ${par_compression:+-l "$par_compression"} \
     ${par_uncompressed:+-u} \
     ${par_minimiser:+-M} \
@@ -40,4 +40,4 @@ $(which samtools) sort \
     "$par_input"
 
 # save text files containing the output of samtools view for later comparison
-$(which samtools) view "$par_output" -o "$par_output".txt
+samtools view "$par_output" -o "$par_output".txt
diff --git a/src/samtools/samtools_sort/test.sh b/src/samtools/samtools_sort/test.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
-test_dir="${meta_resources_dir}test_data"
-out_dir="${meta_resources_dir}test_data/text"
+test_dir="${meta_resources_dir}/test_data"
+out_dir="${meta_resources_dir}/test_data/text"
 
 # Files are compared using the "samtools view" output.
 ############################################################################################