diff --git a/src/samtools/flagstat/config.vsh.yaml b/src/samtools/samtools_flagstat/config.vsh.yaml
similarity index 79%
rename from src/samtools/flagstat/config.vsh.yaml
rename to src/samtools/samtools_flagstat/config.vsh.yaml
index 7850d1b8..20a5e3cd 100644
--- a/src/samtools/flagstat/config.vsh.yaml
+++ b/src/samtools/samtools_flagstat/config.vsh.yaml
@@ -5,9 +5,9 @@ keywords: [ stats, mapping, counts, bam, sam, cram ]
 links:
   homepage: https://www.htslib.org/
   documentation: https://www.htslib.org/doc/samtools-flagstat.html
-  repository: https://github.com/samtools/samtools.git
+  repository: https://github.com/samtools/samtools
 references: 
-  doi: 10.1093/bioinformatics/btp352, 10.1093/gigascience/giab008
+  doi: [10.1093/bioinformatics/btp352, 10.1093/gigascience/giab008]
 license: MIT/Expat
 
 argument_groups:
@@ -44,7 +44,8 @@ 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/flagstat/help.txt b/src/samtools/samtools_flagstat/help.txt
similarity index 100%
rename from src/samtools/flagstat/help.txt
rename to src/samtools/samtools_flagstat/help.txt
diff --git a/src/samtools/flagstat/script.sh b/src/samtools/samtools_flagstat/script.sh
similarity index 65%
rename from src/samtools/flagstat/script.sh
rename to src/samtools/samtools_flagstat/script.sh
index 1d7c8e11..beac3703 100644
--- a/src/samtools/flagstat/script.sh
+++ b/src/samtools/samtools_flagstat/script.sh
@@ -5,9 +5,7 @@
 
 set -e
 
-output_file="$par_output"
-
 samtools flagstat \
     "$par_bam" \
-    > "$output_file"
+    > "$par_output"
     
\ No newline at end of file
diff --git a/src/samtools/flagstat/test.sh b/src/samtools/samtools_flagstat/test.sh
similarity index 100%
rename from src/samtools/flagstat/test.sh
rename to src/samtools/samtools_flagstat/test.sh
diff --git a/src/samtools/flagstat/test_data/a.bam b/src/samtools/samtools_flagstat/test_data/a.bam
similarity index 100%
rename from src/samtools/flagstat/test_data/a.bam
rename to src/samtools/samtools_flagstat/test_data/a.bam
diff --git a/src/samtools/flagstat/test_data/a.bam.bai b/src/samtools/samtools_flagstat/test_data/a.bam.bai
similarity index 100%
rename from src/samtools/flagstat/test_data/a.bam.bai
rename to src/samtools/samtools_flagstat/test_data/a.bam.bai
diff --git a/src/samtools/flagstat/test_data/a_ref.flagstat b/src/samtools/samtools_flagstat/test_data/a_ref.flagstat
similarity index 100%
rename from src/samtools/flagstat/test_data/a_ref.flagstat
rename to src/samtools/samtools_flagstat/test_data/a_ref.flagstat
diff --git a/src/samtools/flagstat/test_data/script.sh b/src/samtools/samtools_flagstat/test_data/script.sh
similarity index 100%
rename from src/samtools/flagstat/test_data/script.sh
rename to src/samtools/samtools_flagstat/test_data/script.sh
diff --git a/src/samtools/flagstat/test_data/test.paired_end.sorted.bam b/src/samtools/samtools_flagstat/test_data/test.paired_end.sorted.bam
similarity index 100%
rename from src/samtools/flagstat/test_data/test.paired_end.sorted.bam
rename to src/samtools/samtools_flagstat/test_data/test.paired_end.sorted.bam
diff --git a/src/samtools/flagstat/test_data/test.paired_end.sorted.bam.bai b/src/samtools/samtools_flagstat/test_data/test.paired_end.sorted.bam.bai
similarity index 100%
rename from src/samtools/flagstat/test_data/test.paired_end.sorted.bam.bai
rename to src/samtools/samtools_flagstat/test_data/test.paired_end.sorted.bam.bai
diff --git a/src/samtools/flagstat/test_data/test_ref.paired_end.sorted.flagstat b/src/samtools/samtools_flagstat/test_data/test_ref.paired_end.sorted.flagstat
similarity index 100%
rename from src/samtools/flagstat/test_data/test_ref.paired_end.sorted.flagstat
rename to src/samtools/samtools_flagstat/test_data/test_ref.paired_end.sorted.flagstat