small changes

viash-hub · Aug 28, 2024 · 8f96180 · 8f96180
1 parent d067d38
commit 8f96180
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Showing 2 changed files with 11 additions and 13 deletions.
diff --git a/src/bcftools/bcftools_stats/config.vsh.yaml b/src/bcftools/bcftools_stats/config.vsh.yaml
@@ -58,7 +58,7 @@ argument_groups:
         alternatives: --first_only
         type: boolean_true
         description: | 
-          Include only 1st allele at multiallelic sites
+          Include only 1st allele at multiallelic sites.
 
       - name: --collapse
         alternatives: --c
@@ -72,7 +72,7 @@ argument_groups:
         alternatives: --d
         type: string
         description: | 
-          Depth distribution: min,max,bin size [0,500,1]
+          Depth distribution: min,max,bin size.
         example: 0,500,1
 
       - name: --exclude
@@ -88,21 +88,19 @@ argument_groups:
         description: | 
           tab-delimited file with exons for indel frameshifts statistics. 
           The columns of the file are CHR, FROM, TO, with 1-based, inclusive, positions. 
-          The file is BGZF-compressed and indexed with tabix
-          e.g. 
-            tabix -s1 -b2 -e3 file.gz
+          The file is BGZF-compressed and indexed with tabix (e.g. tabix -s1 -b2 -e3 file.gz).
 
       - name: --apply_filters
         alternatives: --f
         type: string
         description: | 
-          Require at least one of the listed FILTER strings (e.g. "PASS,.")
+          Require at least one of the listed FILTER strings (e.g. "PASS,.").
 
       - name: --fasta_reference
         alternatives: --F
         type: file
         description: | 
-          Faidx indexed reference sequence file to determine INDEL context
+          Faidx indexed reference sequence file to determine INDEL context.
 
       - name: --include
         alternatives: --i
@@ -115,13 +113,13 @@ argument_groups:
         alternatives: --I
         type: boolean_true
         description: | 
-          Collect stats for sites with ID separately (known vs novel)
+          Collect stats for sites with ID separately (known vs novel).
 
       - name: --regions
         alternatives: --r
         type: string
         description: | 
-          Restrict to comma-separated list of regions
+          Restrict to comma-separated list of regions.
 
       - name: --regions_file
         alternatives: --R
@@ -168,7 +166,7 @@ argument_groups:
         alternatives: --T
         type: file
         description: | 
-          Similar to -R but streams rather than index-jumps.
+          Similar to --regions_file option but streams rather than index-jumps.
 
       - name: --targets_overlaps
         type: string

diff --git a/src/bcftools/bcftools_stats/test.sh b/src/bcftools/bcftools_stats/test.sh
@@ -183,7 +183,7 @@ popd > /dev/null
 # Test 6: Include, Regions
 mkdir "$TMPDIR/test6" && pushd "$TMPDIR/test6" > /dev/null
 
-echo "> Run bcftools_stats on VCF file with include, regions"
+echo "> Run bcftools_stats on VCF file with include and regions options"
 "$meta_executable" \
   --input "../example.vcf.gz" \
   --output "stats.txt" \
@@ -198,10 +198,10 @@ echo "- test6 succeeded -"
 
 popd > /dev/null
 
-# Test 7: Regions Overlap, Samples, Samples File
+# Test 7: Regions Overlap, Samples
 mkdir "$TMPDIR/test7" && pushd "$TMPDIR/test7" > /dev/null
 
-echo "> Run bcftools_stats on VCF file with regions overlap, samples, and samples file"
+echo "> Run bcftools_stats on VCF file with regions overlap, and samples options"
 "$meta_executable" \
   --input "../example.vcf" \
   --output "stats.txt" \