CI
2a330fe450
Build pipeline: viash-hub.biobox.main-62lvg
Source commit: dc7b33d51f
Source message: Bcftools Norm (#144)
* Initial Commit
* config and help.txt
* script.sh
* test template
* More tests and debugging
* test 5 and 6
* test 7, 8, 9
* Update test.sh
* fixing bug on config
* Changelog
* Update config.vsh.yaml
* Requested changes
* Bug fixing
---------
Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com>
359 lines
9.3 KiB
YAML
359 lines
9.3 KiB
YAML
name: "samtools_sort"
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namespace: "samtools"
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version: "main"
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authors:
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- name: "Emma Rousseau"
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roles:
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- "author"
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- "maintainer"
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info:
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links:
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email: "emma@data-intuitive.com"
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github: "emmarousseau"
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linkedin: "emmarousseau1"
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organizations:
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- name: "Data Intuitive"
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href: "https://www.data-intuitive.com"
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role: "Bioinformatician"
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argument_groups:
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- name: "Inputs"
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arguments:
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- type: "file"
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name: "--input"
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description: "SAM/BAM/CRAM input file."
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info: null
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must_exist: true
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create_parent: true
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required: true
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- name: "Outputs"
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arguments:
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- type: "file"
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name: "--output"
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description: "Write final output to file.\n"
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info: null
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example:
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- "out.bam"
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must_exist: true
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create_parent: true
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required: true
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direction: "output"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--output_fmt"
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alternatives:
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- "-O"
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description: "Specify output format (SAM, BAM, CRAM).\n"
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info: null
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example:
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- "BAM"
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--output_fmt_option"
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description: "Specify a single output file format option in the form\nof OPTION\
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\ or OPTION=VALUE.\n"
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--reference"
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description: "Reference sequence FASTA FILE.\n"
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info: null
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example:
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- "ref.fa"
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must_exist: true
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create_parent: true
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "boolean_true"
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name: "--write_index"
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description: "Automatically index the output files.\n"
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info: null
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direction: "input"
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- type: "string"
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name: "--prefix"
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alternatives:
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- "-T"
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description: "Write temporary files to PREFIX.nnnn.bam.\n"
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "boolean_true"
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name: "--no_PG"
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description: "Do not add a PG line.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--template_coordinate"
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description: "Sort by template-coordinate.\n"
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info: null
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direction: "input"
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- type: "string"
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name: "--input_fmt_option"
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description: "Specify a single input file format option in the form\nof OPTION\
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\ or OPTION=VALUE.\n"
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- name: "Options"
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arguments:
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- type: "integer"
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name: "--compression"
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alternatives:
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- "-l"
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description: "Set compression level, from 0 (uncompressed) to 9 (best).\n"
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info: null
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default:
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- 0
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "boolean_true"
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name: "--uncompressed"
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alternatives:
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- "-u"
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description: "Output uncompressed data (equivalent to --compression 0).\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--minimiser"
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alternatives:
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- "-M"
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description: "Use minimiser for clustering unaligned/unplaced reads.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--not_reverse"
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alternatives:
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- "-R"
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description: "Do not use reverse strand (only compatible with --minimiser)\n"
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info: null
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direction: "input"
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- type: "integer"
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name: "--kmer_size"
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alternatives:
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- "-K"
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description: "Kmer size to use for minimiser.\n"
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info: null
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example:
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- 20
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--order"
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alternatives:
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- "-I"
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description: "Order minimisers by their position in FILE FASTA.\n"
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info: null
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example:
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- "ref.fa"
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must_exist: true
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create_parent: true
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "integer"
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name: "--window"
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alternatives:
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- "-w"
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description: "Window size for minimiser INDEXING VIA --order REF.FA.\n"
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info: null
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example:
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- 100
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "boolean_true"
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name: "--homopolymers"
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alternatives:
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- "-H"
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description: "Squash homopolymers when computing minimiser.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--natural_sort"
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alternatives:
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- "-n"
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description: "Sort by read name (natural): cannot be used with samtools index.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--ascii_sort"
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alternatives:
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- "-N"
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description: "Sort by read name (ASCII): cannot be used with samtools index.\n"
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info: null
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direction: "input"
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- type: "string"
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name: "--tag"
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alternatives:
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- "-t"
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description: "Sort by value of TAG. Uses position as secondary index \n(or read\
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\ name if --natural_sort is set).\n"
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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resources:
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- type: "bash_script"
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path: "script.sh"
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is_executable: true
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description: "Sort SAM/BAM/CRAM file."
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test_resources:
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- type: "bash_script"
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path: "test.sh"
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is_executable: true
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- type: "file"
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path: "test_data"
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info: null
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status: "enabled"
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requirements:
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commands:
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- "ps"
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keywords:
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- "sort"
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- "bam"
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- "sam"
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- "cram"
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license: "MIT/Expat"
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references:
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doi:
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- "10.1093/bioinformatics/btp352"
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- "10.1093/gigascience/giab008"
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links:
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repository: "https://github.com/samtools/samtools"
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homepage: "https://www.htslib.org/"
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documentation: "https://www.htslib.org/doc/samtools-sort.html"
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runners:
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- type: "executable"
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id: "executable"
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docker_setup_strategy: "ifneedbepullelsecachedbuild"
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- type: "nextflow"
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id: "nextflow"
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directives:
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tag: "$id"
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auto:
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simplifyInput: true
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simplifyOutput: false
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transcript: false
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publish: false
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config:
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labels:
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mem1gb: "memory = 1000000000.B"
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mem2gb: "memory = 2000000000.B"
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mem5gb: "memory = 5000000000.B"
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mem10gb: "memory = 10000000000.B"
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mem20gb: "memory = 20000000000.B"
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mem50gb: "memory = 50000000000.B"
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mem100gb: "memory = 100000000000.B"
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mem200gb: "memory = 200000000000.B"
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mem500gb: "memory = 500000000000.B"
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mem1tb: "memory = 1000000000000.B"
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mem2tb: "memory = 2000000000000.B"
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mem5tb: "memory = 5000000000000.B"
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mem10tb: "memory = 10000000000000.B"
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mem20tb: "memory = 20000000000000.B"
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mem50tb: "memory = 50000000000000.B"
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mem100tb: "memory = 100000000000000.B"
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mem200tb: "memory = 200000000000000.B"
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mem500tb: "memory = 500000000000000.B"
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mem1gib: "memory = 1073741824.B"
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mem2gib: "memory = 2147483648.B"
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mem4gib: "memory = 4294967296.B"
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mem8gib: "memory = 8589934592.B"
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mem16gib: "memory = 17179869184.B"
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mem32gib: "memory = 34359738368.B"
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mem64gib: "memory = 68719476736.B"
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mem128gib: "memory = 137438953472.B"
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mem256gib: "memory = 274877906944.B"
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mem512gib: "memory = 549755813888.B"
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mem1tib: "memory = 1099511627776.B"
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mem2tib: "memory = 2199023255552.B"
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mem4tib: "memory = 4398046511104.B"
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mem8tib: "memory = 8796093022208.B"
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mem16tib: "memory = 17592186044416.B"
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mem32tib: "memory = 35184372088832.B"
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mem64tib: "memory = 70368744177664.B"
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mem128tib: "memory = 140737488355328.B"
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mem256tib: "memory = 281474976710656.B"
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mem512tib: "memory = 562949953421312.B"
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cpu1: "cpus = 1"
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cpu2: "cpus = 2"
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cpu5: "cpus = 5"
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cpu10: "cpus = 10"
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cpu20: "cpus = 20"
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cpu50: "cpus = 50"
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cpu100: "cpus = 100"
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cpu200: "cpus = 200"
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cpu500: "cpus = 500"
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cpu1000: "cpus = 1000"
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debug: false
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container: "docker"
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engines:
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- type: "docker"
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id: "docker"
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image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1"
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target_registry: "images.viash-hub.com"
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target_tag: "main"
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namespace_separator: "/"
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setup:
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- type: "docker"
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run:
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- "samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \\\nsed 's#Using\
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\ ##;s# \\([0-9\\.]*\\)$#: \\1#' > /var/software_versions.txt\n"
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entrypoint: []
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cmd: null
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- type: "native"
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id: "native"
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build_info:
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config: "src/samtools/samtools_sort/config.vsh.yaml"
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runner: "executable"
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engine: "docker|native"
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output: "target/executable/samtools/samtools_sort"
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executable: "target/executable/samtools/samtools_sort/samtools_sort"
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viash_version: "0.9.0-RC7"
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git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
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git_remote: "https://github.com/viash-hub/biobox"
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package_config:
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name: "biobox"
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version: "main"
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description: "A collection of bioinformatics tools for working with sequence data.\n"
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info: null
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viash_version: "0.9.0-RC7"
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source: "src"
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target: "target"
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config_mods:
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- ".requirements.commands := ['ps']\n"
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- ".engines += { type: \"native\" }"
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- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
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- ".engines[.type == 'docker'].target_tag := 'main'"
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keywords:
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- "bioinformatics"
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- "modules"
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- "sequencing"
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license: "MIT"
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organization: "vsh"
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links:
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repository: "https://github.com/viash-hub/biobox"
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issue_tracker: "https://github.com/viash-hub/biobox/issues"
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