Initial Commint

src/bcftools/bcftools_concat/config.vsh.yaml

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+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