diff --git a/src/bcftools/bcftools_norm/config.vsh.yaml b/src/bcftools/bcftools_norm/config.vsh.yaml index 186d6fbd..377298f6 100644 --- a/src/bcftools/bcftools_norm/config.vsh.yaml +++ b/src/bcftools/bcftools_norm/config.vsh.yaml @@ -3,7 +3,7 @@ namespace: bcftools description: | Left-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows. -keywords: [Annotate, VCF, BCF] +keywords: [Normalize, VCF, BCF] links: homepage: https://samtools.github.io/bcftools/ documentation: https://samtools.github.io/bcftools/bcftools.html#norm @@ -16,7 +16,7 @@ requirements: commands: [bcftools] authors: - __merge__: /src/_authors/theodoro_gasperin.yaml - roles: [ author, maintainer ] + roles: [author] argument_groups: - name: Inputs @@ -112,20 +112,30 @@ argument_groups: description: Annotate modified records with INFO/STR indicating the original variant. - name: --regions - alternatives: -r + alternatives: --r type: string - description: Restrict to comma-separated list of regions. + description: | + Restrict to comma-separated list of regions. + Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]. + example: '20:1000000-2000000' - name: --regions_file - alternatives: -R + alternatives: --R type: file - description: Restrict to regions listed in a file. + description: | + Restrict to regions listed in a file. + Regions can be specified either on a VCF, BED, or tab-delimited file (the default). + For more information check manual. - name: --regions_overlap type: string choices: ['pos', 'record', 'variant', '0', '1', '2'] description: | - Include if POS in the region (0), record overlaps (1), variant overlaps (2). + This option controls how overlapping records are determined: + set to 'pos' or '0' if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); + set to 'record' or '1' if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, + and includes indels with POS at the end of a region, which are technically outside the region); + or set to 'variant' or '2' to include only true overlapping variation (compare the full VCF representation "TA>T-" vs the true sequence variation "A>-"). - name: --site_win alternatives: -w @@ -142,22 +152,19 @@ argument_groups: alternatives: -t type: string description: Similar to -r but streams rather than index-jumps. + example: '20:1000000-2000000' - name: --targets_file alternatives: -T type: file - description: Similar to -R but streams rather than index-jumps. + description: Similar to --regions_file but streams rather than index-jumps. - name: --targets_overlap type: string choices: ['pos', 'record', 'variant', '0', '1', '2'] description: | Include if POS in the region (0), record overlaps (1), variant overlaps (2). - - - name: --threads - type: integer - description: | - Use multithreading with the specified number of worker threads. + Similar to --regions_overlap. resources: - type: bash_script diff --git a/src/bcftools/bcftools_norm/script.sh b/src/bcftools/bcftools_norm/script.sh index 2a9637b1..eb5263d6 100644 --- a/src/bcftools/bcftools_norm/script.sh +++ b/src/bcftools/bcftools_norm/script.sh @@ -42,7 +42,7 @@ bcftools norm \ ${par_targets:+-t "$par_targets"} \ ${par_targets_file:+-T "$par_targets_file"} \ ${par_targets_overlap:+--targets-overlap "$par_targets_overlap"} \ - ${par_threads:+--threads "$par_threads"} \ + ${meta_cpus:+--threads "$meta_cpus"} \\ ${par_output_type:+-O "$par_output_type"} \ -o $par_output \ $par_input