diff --git a/src/bcftools/bcftools_concat/config.vsh.yaml b/src/bcftools/bcftools_concat/config.vsh.yaml new file mode 100644 index 00000000..7f5f5f35 --- /dev/null +++ b/src/bcftools/bcftools_concat/config.vsh.yaml @@ -0,0 +1,185 @@ +name: bcftools_concat +namespace: bcftools +description: | + . +keywords: [Concatenate, VCF, BCF] +links: + homepage: https://samtools.github.io/bcftools/ + documentation: https://samtools.github.io/bcftools/bcftools.html#concat + repository: https://github.com/samtools/bcftools + issue_tracker: https://github.com/samtools/bcftools/issues +references: + doi: https://doi.org/10.1093/gigascience/giab008 +license: MIT/Expat, GNU +requirements: + commands: [bcftools] +authors: + - __merge__: /src/_authors/theodoro_gasperin.yaml + roles: [ author, maintainer ] + +argument_groups: + - name: Inputs + arguments: + - name: --input + alternatives: -i + type: file + multiple: true + description: Input VCF/BCF file. + required: true + + - name: Outputs + arguments: + - name: --output + alternatives: -o + direction: output + type: file + description: Output concatenated VCF/BCF file. + required: true + + - name: Options + arguments: + + # - name: --atomize + # alternatives: -a + # type: boolean_true + # description: | + # Decompose complex variants (e.g., MNVs become consecutive SNVs). + + # - name: --atom_overlaps + # type: string + # choices: [".", "*"] + # description: | + # Use the star allele (*) for overlapping alleles or set to missing (.). + + # - name: --check_ref + # alternatives: -c + # type: string + # choices: ['e', 'w', 'x', 's'] + # description: | + # Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites. + + # - name: --remove_duplicates + # alternatives: -d + # type: string + # choices: ['snps', 'indels', 'both', 'all', 'exact', 'none'] + # description: Remove duplicate snps, indels, both, all, exact matches, or none (old -D option). + + # - name: --fasta_ref + # alternatives: -f + # type: file + # description: Reference fasta sequence file. + + # - name: --force + # type: boolean_true + # description: | + # Try to proceed even if malformed tags are encountered. + # Experimental, use at your own risk. + + # - name: --keep_sum + # type: string + # description: | + # Keep vector sum constant when splitting multiallelics (see github issue #360). + + # - name: --multiallelics + # alternatives: -m + # type: string + # choices: ['+snps', '+indels', '+both', '+any', '-snps', '-indels', '-both', '-any'] + # description: | + # Split multiallelics (-) or join biallelics (+), type: snps, indels, both, any [default: both]. + + # - name: --no_version + # type: boolean_true + # description: Do not append version and command line information to the header. + + # - name: --do_not_normalize + # alternatives: -N + # type: boolean_true + # description: Do not normalize indels (with -m or -c s). + + # - name: --output_type + # alternatives: --O + # type: string + # choices: ['u', 'z', 'b', 'v'] + # description: | + # Output type: + # u: uncompressed BCF + # z: compressed VCF + # b: compressed BCF + # v: uncompressed VCF + + # - name: --old_rec_tag + # type: string + # description: Annotate modified records with INFO/STR indicating the original variant. + + # - name: --regions + # alternatives: -r + # type: string + # description: Restrict to comma-separated list of regions. + + # - name: --regions_file + # alternatives: -R + # type: file + # description: Restrict to regions listed in a file. + + # - 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). + + # - name: --site_win + # alternatives: -w + # type: integer + # description: | + # Buffer for sorting lines that changed position during realignment. + + # - name: --strict_filter + # alternatives: -s + # type: boolean_true + # description: When merging (-m+), merged site is PASS only if all sites being merged PASS. + + # - name: --targets + # alternatives: -t + # type: string + # description: Similar to -r but streams rather than index-jumps. + + # - name: --targets_file + # alternatives: -T + # type: file + # description: Similar to -R 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. + +resources: + - type: bash_script + path: script.sh + +test_resources: + - type: bash_script + path: test.sh + +engines: + - type: docker + image: debian:stable-slim + setup: + - type: apt + packages: [bcftools, procps] + - type: docker + run: | + echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\"" > /var/software_versions.txt + test_setup: + - type: apt + packages: [tabix] + +runners: + - type: executable + - type: nextflow \ No newline at end of file diff --git a/src/bcftools/bcftools_concat/script.sh b/src/bcftools/bcftools_concat/script.sh new file mode 100644 index 00000000..e69de29b diff --git a/src/bcftools/bcftools_concat/test.sh b/src/bcftools/bcftools_concat/test.sh new file mode 100644 index 00000000..e69de29b