From 92a1645dd28e189f45716594f27f980e2be13cd0 Mon Sep 17 00:00:00 2001
From: emmarousseau <emmarou1@icloud.com>
Date: Thu, 11 Apr 2024 11:13:34 +0100
Subject: [PATCH] Minor changes, paths, config and script

---
 CHANGELOG.md                                | 6 +++---
 src/samtools/samtools_index/config.vsh.yaml | 2 +-
 src/samtools/samtools_index/script.sh       | 2 +-
 src/samtools/samtools_index/test.sh         | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ae53d570..dd8d0a48 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -36,9 +36,9 @@
     - `salmon/salmon_quant`: Transcript quantification from RNA-seq data (PR #24).
 
 * `samtools`:
-    - `samtools/flagstat`: Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type (PR #31).
-    - `samtools/idxstats`: Reports alignment summary statistics for a SAM/BAM/CRAM file (PR #32).
-    - `samtools/index`: Index SAM/BAM/CRAM files (PR #35).
+    - `samtools/samtools_flagstat`: Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type (PR #31).
+    - `samtools/samtools_idxstats`: Reports alignment summary statistics for a SAM/BAM/CRAM file (PR #32).
+    - `samtools/samtools_index`: Index SAM/BAM/CRAM files (PR #35).
 
 ## MAJOR CHANGES
 
diff --git a/src/samtools/samtools_index/config.vsh.yaml b/src/samtools/samtools_index/config.vsh.yaml
index 88c68ebd..8c59a20e 100644
--- a/src/samtools/samtools_index/config.vsh.yaml
+++ b/src/samtools/samtools_index/config.vsh.yaml
@@ -25,7 +25,7 @@ argument_groups:
         type: file
         description: Output file name
         required: true
-        must_exist: false
+        direction: output
         example: out.bam.bai
   - name: Options
     arguments:
diff --git a/src/samtools/samtools_index/script.sh b/src/samtools/samtools_index/script.sh
index bc5066cb..9db47fa4 100644
--- a/src/samtools/samtools_index/script.sh
+++ b/src/samtools/samtools_index/script.sh
@@ -9,7 +9,7 @@ set -e
 [[ "$par_csi" == "false" ]] && unset par_csi
 [[ "$par_multiple" == "false" ]] && unset par_multiple
 
-$(which samtools) index \
+samtools index \
     "$par_input" \
     ${par_csi:+-c} \
     ${par_bai:+-b} \
diff --git a/src/samtools/samtools_index/test.sh b/src/samtools/samtools_index/test.sh
index fd3ea87f..f4b1d3b6 100644
--- a/src/samtools/samtools_index/test.sh
+++ b/src/samtools/samtools_index/test.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-test_dir="${meta_resources_dir}test_data"
+test_dir="${meta_resources_dir}/test_data"
 
 echo ">>> Testing $meta_functionality_name"