CI
db2f4203b8
Build pipeline: viash-hub.biobox.main-n2mwd
Source commit: c3ba4a7849
Source message: Bcftools annotate (#143)
* Initial commit
* Update config.vsh.yaml
* changes in config file
* Update script.sh
* Help File
* Update script.sh
* Update test.sh
* bug fixing and adding tests
* Update test.sh
* Update test.sh
* adding 3rd test
* More tests
* Moreee tests
* Update test.sh
* small changes
* Update CHANGELOG.md
* Update config.vsh.yaml
* bug fixing on config
* Requested changes
---------
Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com>
428 lines
11 KiB
YAML
428 lines
11 KiB
YAML
name: "samtools_stats"
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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: "Input file.\n"
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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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- type: "file"
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name: "--bai"
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description: "Index file.\n"
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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: 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: "--fasta"
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description: "Reference file the CRAM was created with.\n"
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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: 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: "--coverage"
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alternatives:
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- "-c"
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description: "Coverage distribution min;max;step. Default: [1, 1000, 1].\n"
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info: null
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example:
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- 1
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- 1000
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- 1
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required: false
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direction: "input"
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multiple: true
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multiple_sep: ";"
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- type: "boolean_true"
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name: "--remove_dups"
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alternatives:
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- "-d"
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description: "Exclude from statistics reads marked as duplicates.\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: "--customized_index_file"
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alternatives:
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- "-X"
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description: "Use a customized index file.\n"
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info: null
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direction: "input"
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- type: "string"
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name: "--required_flag"
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alternatives:
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- "-f"
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description: "Required flag, 0 for unset. See also `samtools flags`. Default:\
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\ `\"0\"`.\n"
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info: null
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example:
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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: "string"
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name: "--filtering_flag"
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alternatives:
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- "-F"
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description: "Filtering flag, 0 for unset. See also `samtools flags`. Default:\
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\ `0`.\n"
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info: null
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example:
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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: "double"
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name: "--GC_depth"
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description: "The size of GC-depth bins (decreasing bin size increases memory\
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\ requirement). Default: `20000`.\n"
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info: null
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example:
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- 20000.0
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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: "integer"
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name: "--insert_size"
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alternatives:
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- "-i"
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description: "Maximum insert size. Default: `8000`.\n"
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info: null
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example:
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- 8000
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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: "--id"
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alternatives:
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- "-I"
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description: "Include only listed read group or sample name.\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: "integer"
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name: "--read_length"
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alternatives:
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- "-l"
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description: "Include in the statistics only reads with the given read length.\
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\ Default: `-1`.\n"
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info: null
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example:
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- -1
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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: "double"
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name: "--most_inserts"
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alternatives:
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- "-m"
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description: "Report only the main part of inserts. Default: `0.99`.\n"
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info: null
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example:
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- 0.99
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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: "--split_prefix"
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alternatives:
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- "-P"
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description: "Path or string prefix for filepaths output by --split (default is\
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\ input filename).\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: "integer"
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name: "--trim_quality"
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alternatives:
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- "-q"
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description: "The BWA trimming parameter. Default: `0`.\n"
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info: null
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example:
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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: "file"
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name: "--ref_seq"
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alternatives:
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- "-r"
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description: "Reference sequence (required for GC-depth and mismatches-per-cycle\
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\ calculation).\n"
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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: 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: "--split"
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alternatives:
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- "-S"
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description: "Also write statistics to separate files split by tagged field.\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: "--target_regions"
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alternatives:
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- "-t"
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description: "Do stats in these regions only. Tab-delimited file chr,from,to,\
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\ 1-based, inclusive.\n"
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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: 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: "--sparse"
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alternatives:
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- "-x"
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description: "Suppress outputting IS rows where there are no insertions.\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: "--remove_overlaps"
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alternatives:
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- "-p"
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description: "Remove overlaps of paired-end reads from coverage and base count\
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\ computations.\n"
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info: null
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direction: "input"
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- type: "integer"
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name: "--cov_threshold"
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alternatives:
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- "-g"
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description: "Only bases with coverage above this value will be included in the\
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\ target percentage computation. Default: `0`.\n"
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info: null
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example:
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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: "string"
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name: "--input_fmt_option"
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description: "Specify a single input file format option in the form of 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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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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- name: "Outputs"
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arguments:
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- type: "file"
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name: "--output"
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alternatives:
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- "-o"
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description: "Output file.\n"
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info: null
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example:
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- "out.txt"
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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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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: "Reports alignment summary statistics for a BAM 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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- "statistics"
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- "counts"
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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-stats.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_stats/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_stats"
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executable: "target/executable/samtools/samtools_stats/samtools_stats"
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viash_version: "0.9.0-RC7"
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git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
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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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