diff --git a/src/samtools/idxstats/help.txt b/src/samtools/idxstats/help.txt
deleted file mode 100644
index c0fb5947..00000000
--- a/src/samtools/idxstats/help.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-```
-samtools idxstats
-```
-
-Usage: samtools idxstats <in.bam>
\ No newline at end of file
diff --git a/src/samtools/idxstats/config.vsh.yaml b/src/samtools/samtools_idxstats/config.vsh.yaml
similarity index 86%
rename from src/samtools/idxstats/config.vsh.yaml
rename to src/samtools/samtools_idxstats/config.vsh.yaml
index 338c59c6..781bd8be 100644
--- a/src/samtools/idxstats/config.vsh.yaml
+++ b/src/samtools/samtools_idxstats/config.vsh.yaml
@@ -5,7 +5,7 @@ keywords: [stats, mapping, counts, chromosome, bam, sam, cram]
 links:
   homepage: https://www.htslib.org/
   documentation: https://www.htslib.org/doc/samtools-idxstats.html
-  repository: https://github.com/samtools/samtools.git
+  repository: https://github.com/samtools/samtools
 references: 
   doi: 10.1093/bioinformatics/btp352, 10.1093/gigascience/giab008
 license: MIT/Expat
@@ -46,7 +46,8 @@ engines:
     setup:
       - type: docker
         run: |
-          echo "$(samtools --version 2>&1)" > /var/software_versions.txt
+          samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
+          sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 runners:
 - type: executable
 - type: nextflow
\ No newline at end of file
diff --git a/src/samtools/samtools_idxstats/help.txt b/src/samtools/samtools_idxstats/help.txt
new file mode 100644
index 00000000..7b63ab17
--- /dev/null
+++ b/src/samtools/samtools_idxstats/help.txt
@@ -0,0 +1,12 @@
+```
+samtools idxstats
+```
+
+Usage: samtools idxstats [options] <in.bam>
+      --input-fmt-option OPT[=VAL]
+               Specify a single input file format option in the form
+               of OPTION or OPTION=VALUE
+  -@, --threads INT
+               Number of additional threads to use [0]
+      --verbosity INT
+               Set level of verbosity
\ No newline at end of file
diff --git a/src/samtools/idxstats/script.sh b/src/samtools/samtools_idxstats/script.sh
similarity index 100%
rename from src/samtools/idxstats/script.sh
rename to src/samtools/samtools_idxstats/script.sh
diff --git a/src/samtools/idxstats/test.sh b/src/samtools/samtools_idxstats/test.sh
similarity index 100%
rename from src/samtools/idxstats/test.sh
rename to src/samtools/samtools_idxstats/test.sh
diff --git a/src/samtools/idxstats/test_data/a.sorted.bam b/src/samtools/samtools_idxstats/test_data/a.sorted.bam
similarity index 100%
rename from src/samtools/idxstats/test_data/a.sorted.bam
rename to src/samtools/samtools_idxstats/test_data/a.sorted.bam
diff --git a/src/samtools/idxstats/test_data/a.sorted.bam.bai b/src/samtools/samtools_idxstats/test_data/a.sorted.bam.bai
similarity index 100%
rename from src/samtools/idxstats/test_data/a.sorted.bam.bai
rename to src/samtools/samtools_idxstats/test_data/a.sorted.bam.bai
diff --git a/src/samtools/idxstats/test_data/a_ref.sorted.idxstats b/src/samtools/samtools_idxstats/test_data/a_ref.sorted.idxstats
similarity index 100%
rename from src/samtools/idxstats/test_data/a_ref.sorted.idxstats
rename to src/samtools/samtools_idxstats/test_data/a_ref.sorted.idxstats
diff --git a/src/samtools/idxstats/test_data/script.sh b/src/samtools/samtools_idxstats/test_data/script.sh
similarity index 100%
rename from src/samtools/idxstats/test_data/script.sh
rename to src/samtools/samtools_idxstats/test_data/script.sh
diff --git a/src/samtools/idxstats/test_data/test.paired_end.sorted.bam b/src/samtools/samtools_idxstats/test_data/test.paired_end.sorted.bam
similarity index 100%
rename from src/samtools/idxstats/test_data/test.paired_end.sorted.bam
rename to src/samtools/samtools_idxstats/test_data/test.paired_end.sorted.bam
diff --git a/src/samtools/idxstats/test_data/test.paired_end.sorted.bam.bai b/src/samtools/samtools_idxstats/test_data/test.paired_end.sorted.bam.bai
similarity index 100%
rename from src/samtools/idxstats/test_data/test.paired_end.sorted.bam.bai
rename to src/samtools/samtools_idxstats/test_data/test.paired_end.sorted.bam.bai
diff --git a/src/samtools/idxstats/test_data/test_ref.paired_end.sorted.idxstats b/src/samtools/samtools_idxstats/test_data/test_ref.paired_end.sorted.idxstats
similarity index 100%
rename from src/samtools/idxstats/test_data/test_ref.paired_end.sorted.idxstats
rename to src/samtools/samtools_idxstats/test_data/test_ref.paired_end.sorted.idxstats