diff --git a/src/bgzip/config.vsh.yaml b/src/bgzip/config.vsh.yaml index 159c33e8..c37db43c 100644 --- a/src/bgzip/config.vsh.yaml +++ b/src/bgzip/config.vsh.yaml @@ -6,6 +6,8 @@ functionality: documentation: https://www.htslib.org/doc/bgzip.html repository: https://github.com/samtools/htslib licence: MIT + reference: + doi: 10.1093/gigascience/giab007 requirements: commands: [ bgzip ] argument_groups: @@ -30,7 +32,7 @@ functionality: description: name of BGZF index file [file.gz.gzi] - name: Arguments arguments: - - name: offset + - name: --offset alternatives: -b type: integer description: decompress at virtual file pointer (0-based uncompressed offset) @@ -79,6 +81,7 @@ functionality: [[ "$par_binary" == "false" ]] && unset par_binary bgzip -c \ ${meta_cpus:+--threads "${meta_cpus}"} \ + ${par_offset:+-b "${par_offset}"} \ ${par_decompress:+-d} \ ${par_rebgzip:+-g} \ ${par_index:+-i} \ @@ -87,6 +90,7 @@ functionality: ${par_reindex:+-r} \ ${par_size:+-s "${par_size}"} \ ${par_test:+-t} \ + ${par_binary:+--binary} \ "$par_input" > "$par_output" test_resources: - type: bash_script