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src/bcftools/bcftools_norm/config.vsh.yaml

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+name: bcftools_norm
+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]
+links:
+  homepage: https://samtools.github.io/bcftools/
+  documentation: https://samtools.github.io/bcftools/bcftools.html#norm
+  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 annotated file.
+        required: true
+
+  - name: Options
+    description: | 
+      For examples on how to use use bcftools annotate see http://samtools.github.io/bcftools/howtos/annotate.html.
+      For more details on the options see https://samtools.github.io/bcftools/bcftools.html#annotate.
+    arguments:
+
+      - name: --annotations
+        alternatives: --a
+        type: file
+        description: | 
+          VCF file or tabix-indexed FILE with annotations: CHR\tPOS[\tVALUE]+ . 
+
+      - name: --columns
+        alternatives: --c
+        type: string
+        description: | 
+          List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. 
+          See man page for details.
+
+      - name: --columns_file
+        alternatives: --C
+        type: file
+        description: | 
+          Read -c columns from FILE, one name per row, with optional --merge_logic TYPE: NAME[ TYPE].
+
+      - name: --exclude
+        alternatives: --e
+        type: string
+        description: | 
+          Exclude sites for which the expression is true.
+          See https://samtools.github.io/bcftools/bcftools.html#expressions for details.
+
+      - name: --force
+        type: boolean_true
+        description: | 
+          continue even when parsing errors, such as undefined tags, are encountered. 
+          Note this can be an unsafe operation and can result in corrupted BCF files. 
+          If this option is used, make sure to sanity check the result thoroughly.
+
+      - name: --header_line
+        alternatives: --H
+        type: string
+        description: | 
+          Header line which should be appended to the VCF header, can be given multiple times.
+
+      - name: --header_lines
+        alternatives: --h
+        type: file
+        description: | 
+          File with header lines to append to the VCF header.
+          For example:
+            ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description="Example header line">
+            ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description="Yet another header line">
+
+      - name: --set_id
+        alternatives: --I
+        type: string
+        description: | 
+          Set ID column using a `bcftools query`-like expression, see man page for details.
+
+      - name: --include
+        type: string
+        description: | 
+          Select sites for which the expression is true.
+          See https://samtools.github.io/bcftools/bcftools.html#expressions for details.
+      
+      - name: --keep_sites
+        alternatives: --k
+        type: boolean_true
+        description: | 
+          Leave --include/--exclude sites unchanged instead of discarding them.
+
+      - name: --merge_logic
+        alternatives: --l
+        type: string
+        description: | 
+          When multiple regions overlap a single record, this option defines how to treat multiple annotation values.
+          See man page for more details.
+
+      - name: --mark_sites
+        alternatives: --m
+        type: string
+        description: | 
+          Annotate sites which are present ("+") or absent ("-") in the -a file with a new INFO/TAG flag.
+
+      - name: --min_overlap
+        type: string
+        description: | 
+          Minimum overlap required as a fraction of the variant in the annotation -a file (ANN), 
+          in the target VCF file (:VCF), or both for reciprocal overlap (ANN:VCF). 
+          By default overlaps of arbitrary length are sufficient. 
+          The option can be used only with the tab-delimited annotation -a file and with BEG and END columns present.
+
+      - name: --no_version
+        type: boolean_true
+        description: | 
+          Do not append version and command line information to the output VCF header.
+
+      - 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: --pair_logic
+        type: string
+        choices: ['snps', 'indels', 'both', 'all', 'some', 'exact']
+        description: | 
+          Controls how to match records from the annotation file to the target VCF. 
+          Effective only when -a is a VCF or BCF file. 
+          The option replaces the former uninuitive --collapse. 
+          See Common Options for more.
+
+      - name: --regions
+        alternatives: --r
+        type: string
+        description: | 
+          Restrict to comma-separated list of regions.
+          See man page for details.
+
+      - name: --regions_file
+        alternatives: --R
+        type: string
+        description: | 
+          Restrict to regions listed in a file.
+          See man page for details.
+
+      - name: --regions_overlap
+        type: string
+        choices: ['pos', 'record', 'variant', '1', '2', '3']
+        description: | 
+          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: --rename_annotations 
+        type: file
+        description: | 
+          Rename annotations: TYPE/old\tnew, where TYPE is one of FILTER,INFO,FORMAT.
+
+      - name: --rename_chromosomes
+        type: file
+        description: | 
+          Rename chromosomes according to the map in file, with "old_name new_name\n" pairs 
+          separated by whitespaces, each on a separate line.
+
+      - name: --samples
+        type: string
+        description: | 
+          Subset of samples to annotate.
+          See also https://samtools.github.io/bcftools/bcftools.html#common_options.
+
+      - name: --samples_file
+        type: file
+        description: | 
+          Subset of samples to annotate in file format.
+          See also https://samtools.github.io/bcftools/bcftools.html#common_options.
+
+      - name: --single_overlaps
+        type: boolean_true
+        description: | 
+          Use this option to keep memory requirements low with very large annotation files. 
+          Note, however, that this comes at a cost, only single overlapping intervals are considered in this mode. 
+          This was the default mode until the commit af6f0c9 (Feb 24 2019).
+
+      - name: --threads
+        type: integer
+        description: | 
+          Number of extra output compression threads.
+          See https://samtools.github.io/bcftools/bcftools.html#common_options.
+
+      - name: --remove
+        alternatives: --x
+        type: string
+        description: | 
+          List of annotations to remove. 
+          Use "FILTER" to remove all filters or "FILTER/SomeFilter" to remove a specific filter. 
+          Similarly, "INFO" can be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT. 
+          To remove all INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER). 
+          "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT".
+
+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
+
+