name: "freebayes"
namespace: "genetic_demux"
version: "v4.0.1"
authors:
- name: "Xichen Wu"
  roles:
  - "author"
  info:
    role: "Contributor"
    links:
      github: "wxicu"
      linkedin: "xichen-wu"
      orcid: "0009-0008-2168-4508"
    organizations:
    - name: "Helmholtz Munich"
      href: "https://www.helmholtz-munich.de"
      role: "Student Assistant"
argument_groups:
- name: "Input"
  arguments:
  - type: "file"
    name: "--bam"
    description: "Add FILE to the set of BAM files to be analyzed."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bam_list"
    description: "A file containing a list of BAM files to be analyzed."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--stdin"
    description: "Read BAM input on stdin."
    info: null
    direction: "input"
  - type: "file"
    name: "--fasta_reference"
    description: "Use FILE as the reference sequence for analysis. An index file (FILE.fai)\
      \ will be created if none exists. If neither --targets nor --region are specified,\
      \ FreeBayes will analyze every position in this reference."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--fasta_reference_index"
    description: "Use FILE.fai as the index of reference sequence for analysis."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--targets"
    description: "Limit analysis to targets listed in the BED-format FILE."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--region"
    description: "Limit analysis to the specified region, 0-base coordinates, end_position\
      \ not included (same as BED format)."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--samples"
    description: "Limit analysis to samples listed (one per line) in the FILE. By\
      \ default FreeBayes will analyze all samples in its input BAM files."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--populations"
    description: "Each line of FILE should list a sample and a population which it\
      \ is part of. The population-based bayesian inference model will then be partitioned\
      \ on the basis of the populations."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--cnv_map"
    description: "Read a copy number map from the BED file FILE, which has either\
      \ a sample-level ploidy or a region-specific format."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--gvcf"
    description: "Write gVCF output, which indicates coverage in uncalled regions."
    info: null
    direction: "input"
  - type: "integer"
    name: "--gvcf_chunk"
    description: "When writing gVCF output emit a record for every NUM bases."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--variant_input"
    description: "Use variants reported in VCF file as input to the algorithm. Variants\
      \ in this file will included in the output even if there is not enough support\
      \ in the data to pass input filters."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--only_use_input_alleles"
    description: "Only provide variant calls and genotype likelihoods for sites and\
      \ alleles which are provided in the VCF input, and provide output in the VCF\
      \ for all input alleles, not just those which have support in the data."
    info: null
    direction: "input"
  - type: "file"
    name: "--haplotype_basis_alleles"
    description: "When specified, only variant alleles provided in this input VCF\
      \ will be used for the construction of complex or haplotype alleles."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--report_all_haplotype_alleles"
    description: "At sites where genotypes are made over haplotype alleles, provide\
      \ information about all alleles in output, not only those which are called."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--report_monomorphic"
    description: "Report even loci which appear to be monomorphic, and report all\
      \ considered alleles, even those which are not in called genotypes."
    info: null
    direction: "input"
  - type: "double"
    name: "--pvar"
    description: "Report sites if the probability that there is a polymorphism at\
      \ the site is greater than N. Note that post-filtering is generally recommended\
      \ over the use of this parameter."
    info: null
    default:
    - 0.0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--strict_vcf"
    description: "Generate strict VCF format (FORMAT/GQ will be an int)."
    info: null
    direction: "input"
  - type: "double"
    name: "--theta"
    description: "The expected mutation rate or pairwise nucleotide diversity among\
      \ the population under analysis. This serves as the single parameter to the\
      \ Ewens Sampling Formula prior model."
    info: null
    default:
    - 0.001
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--ploidy"
    description: "Sets the default ploidy for the analysis to N."
    info: null
    default:
    - 2
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--pooled_discrete"
    description: "Assume that samples result from pooled sequencing. Model pooled\
      \ samples using discrete genotypes across pools."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--pooled_continuous"
    description: "Output all alleles which pass input filters, regardles of genotyping\
      \ outcome or model."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--use_reference_allele"
    description: "This flag includes the reference allele in the analysis as if it\
      \ is another sample from the same population."
    info: null
    direction: "input"
  - type: "string"
    name: "--reference_quality"
    description: "Assign mapping quality of MQ to the reference allele at each site\
      \ and base quality of BQ."
    info: null
    default:
    - "100,60"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--throw_away_snp_obs"
    description: "Ignore SNP alleles."
    info: null
    direction: "input"
  - type: "boolean_false"
    name: "--throw_away_mnps_obs"
    description: "Ignore multi-nuceotide polymorphisms, MNPs. MNPs are excluded as\
      \ default."
    info: null
    direction: "input"
  - type: "boolean_false"
    name: "--throw_away_indel_obs"
    description: "Ignore insertion and deletion alleles. Indels are excluded as default."
    info: null
    direction: "input"
  - type: "boolean_false"
    name: "--throw_away_complex_obs"
    description: "Ignore complex events (composites of other classes). Complex are\
      \ excluded as default"
    info: null
    direction: "input"
  - type: "integer"
    name: "--use_best_n_alleles"
    description: "Evaluate only the best N SNP alleles, ranked by sum of supporting\
      \ quality scores."
    info: null
    default:
    - 0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--max_complex_gap"
    description: "Allow haplotype calls with contiguous embedded matches of up to\
      \ this length."
    info: null
    default:
    - 3
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--min_repeat_size"
    description: "When assembling observations across repeats, require the total repeat\
      \ length at least this many bp."
    info: null
    default:
    - 5
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--min_repeat_entropy"
    description: "To detect interrupted repeats, build across sequence until it has\
      \ entropy > N bits per bp. Set to 0 to turn off."
    info: null
    default:
    - 1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--no_partial_observations"
    description: "Exclude observations which do not fully span the dynamically-determined\
      \ detection window.  (default, use all observations, dividing partial support\
      \ across matching haplotypes when generating haplotypes.)"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--dont_left_align_indels"
    description: "Turn off left-alignment of indels, which is enabled by default."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--use_duplicate_reads"
    description: "Include duplicate-marked alignments in the analysis. default: exclude\
      \ duplicates marked as such in alignments"
    info: null
    direction: "input"
  - type: "integer"
    name: "--min_mapping_quality"
    description: "Exclude alignments from analysis if they have a mapping quality\
      \ less than Q."
    info: null
    default:
    - 1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--min_base_quality"
    description: "Exclude alleles from analysis if their supporting base quality is\
      \ less than Q. Default value is changed according to the instruction of scSplit."
    info: null
    default:
    - 1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--min_supporting_allele_qsum"
    description: "Consider any allele in which the sum of qualities of supporting\
      \ observations is at least Q."
    info: null
    default:
    - 0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--min_supporting_mapping_qsum"
    description: "Consider any allele in which and the sum of mapping qualities of\
      \ supporting reads is at least."
    info: null
    default:
    - 0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--mismatch_base_quality_threshold"
    description: "Count mismatches toward --read-mismatch-limit if the base quality\
      \ of the mismatch is >= Q."
    info: null
    default:
    - 10
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "double"
    name: "--read_max_mismatch_fraction"
    description: "Exclude reads with more than N mismatches where each mismatch has\
      \ base quality >= mismatch-base-quality-threshold."
    info: null
    default:
    - 1.0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--read_mismatch_limit"
    description: "Exclude reads with more than N [0,1] fraction of mismatches where\
      \ each mismatch has base quality >= mismatch-base-quality-threshold."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--read_snp_limit"
    description: "Exclude reads with more than N base mismatches, ignoring gaps with\
      \ quality >= mismatch-base-quality-threshold."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--read_indel_limit"
    description: "Exclude reads with more than N separate gaps."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--standard_filters"
    description: "Use stringent input base and mapping quality filters, equivalent\
      \ to -m 30 -q 20 -R 0 -S 0"
    info: null
    direction: "input"
  - type: "double"
    name: "--min_alternate_fraction"
    description: "Require at least this fraction of observations supporting an alternate\
      \ allele within a single individual in order to evaluate the position."
    info: null
    default:
    - 0.05
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--min_alternate_count"
    description: "Require at least this count of observations supporting an alternate\
      \ allele within a single individual in order to evaluate the position."
    info: null
    default:
    - 2
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--min_alternate_qsum"
    description: "Require at least this sum of quality of observations supporting\
      \ an alternate allele within a single individual in order to evaluate the position."
    info: null
    default:
    - 0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--min_alternate_total"
    description: "Require at least this count of observations supporting an alternate\
      \ allele within the total population in order to use the allele in analysis."
    info: null
    default:
    - 1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--min_coverage"
    description: "Require at least this coverage to process a site."
    info: null
    default:
    - 0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--max_coverage"
    description: "Do not process sites with greater than this coverage."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--no_population_priors"
    description: "Equivalent to --pooled-discrete --hwe-priors-off and removal of\
      \ Ewens Sampling Formula component of priors."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--hwe_priors_off"
    description: "Disable estimation of the probability of the combination arising\
      \ under HWE given the allele frequency as estimated by observation frequency."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--binomial_obs_priors_off"
    description: "Disable incorporation of prior expectations about observations.\
      \ Uses read placement probability, strand balance probability, and read position\
      \ probability."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--allele_balance_priors_off"
    description: "Disable use of aggregate probability of observation balance between\
      \ alleles as a component of the priors."
    info: null
    direction: "input"
  - type: "file"
    name: "--observation_bias"
    description: "Read length-dependent allele observation biases from FILE. The format\
      \ is [length] [alignment efficiency relative to reference] where the efficiency\
      \ is 1 if there is no relative observation bias."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--base_quality_cap"
    description: "Limit estimated observation quality by capping base quality at Q."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "double"
    name: "--prob_contamination"
    description: "An estimate of contamination to use for all samples."
    info: null
    default:
    - 1.0E-8
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--legacy_gls"
    description: "Use legacy (polybayes equivalent) genotype likelihood calculations"
    info: null
    direction: "input"
  - type: "file"
    name: "--contamination_estimates"
    description: "A file containing per-sample estimates of contamination, such as\
      \ those generated by VerifyBamID."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--report_genotype_likelihood_max"
    description: "Report genotypes using the maximum-likelihood estimate provided\
      \ from genotype likelihoods."
    info: null
    direction: "input"
  - type: "integer"
    name: "--genotyping_max_iterations"
    description: "Iterate no more than N times during genotyping step."
    info: null
    default:
    - 1000
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--genotyping_max_banddepth"
    description: "Integrate no deeper than the Nth best genotype by likelihood when\
      \ genotyping."
    info: null
    default:
    - 6
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--posterior_integration_limits"
    description: "Integrate all genotype combinations in our posterior space which\
      \ include no more than N samples with their Mth best data likelihood."
    info: null
    default:
    - "1,3"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--exclude_unobserved_genotypes"
    description: "Skip sample genotypings for which the sample has no supporting reads."
    info: null
    direction: "input"
  - type: "integer"
    name: "--genotype_variant_threshold"
    description: "Limit posterior integration to samples where the second-best genotype\
      \ likelihood is no more than log(N) from the highest genotype likelihood for\
      \ the sample."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--use_mapping_quality"
    description: "Use mapping quality of alleles when calculating data likelihoods."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--harmonic_indel_quality"
    description: "Use a weighted sum of base qualities around an indel, scaled by\
      \ the distance from the indel. By default use a minimum BQ in flanking sequence."
    info: null
    direction: "input"
  - type: "double"
    name: "--read_dependence_factor"
    description: "Incorporate non-independence of reads by scaling successive observations\
      \ by this factor during data likelihood calculations."
    info: null
    default:
    - 0.9
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--genotype_qualities"
    description: "Calculate the marginal probability of genotypes and report as GQ\
      \ in each sample field in the VCF output."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--debug"
    description: "Print debugging output."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--dd"
    description: "Print more verbose debugging output"
    info: null
    direction: "input"
- name: "Output"
  arguments:
  - type: "file"
    name: "--output"
    alternatives:
    - "-o"
    description: "Output directory"
    info: null
    example:
    - "freebayes_out"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--vcf"
    description: "Output VCF-format results to FILE."
    info: null
    example:
    - "snp.vcf"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
- type: "file"
  path: "nextflow_labels.config"
  dest: "nextflow_labels.config"
description: "Freebayes is a Bayesian genetic variant detector designed to\nfind small\
  \ polymorphisms, specifically SNPs.\n"
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
- type: "file"
  path: "demuxafy_test_data"
- type: "file"
  path: "cellranger_tiny_fastq"
info: null
status: "enabled"
scope:
  image: "public"
  target: "public"
license: "MIT"
links:
  repository: "https://github.com/openpipelines-bio/openpipeline"
  docker_registry: "ghcr.io"
runners:
- type: "executable"
  id: "executable"
  docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
  id: "nextflow"
  directives:
    label:
    - "highmem"
    - "highcpu"
    tag: "$id"
  auto:
    simplifyInput: true
    simplifyOutput: false
    transcript: false
    publish: false
  config:
    labels:
      mem1gb: "memory = 1000000000.B"
      mem2gb: "memory = 2000000000.B"
      mem5gb: "memory = 5000000000.B"
      mem10gb: "memory = 10000000000.B"
      mem20gb: "memory = 20000000000.B"
      mem50gb: "memory = 50000000000.B"
      mem100gb: "memory = 100000000000.B"
      mem200gb: "memory = 200000000000.B"
      mem500gb: "memory = 500000000000.B"
      mem1tb: "memory = 1000000000000.B"
      mem2tb: "memory = 2000000000000.B"
      mem5tb: "memory = 5000000000000.B"
      mem10tb: "memory = 10000000000000.B"
      mem20tb: "memory = 20000000000000.B"
      mem50tb: "memory = 50000000000000.B"
      mem100tb: "memory = 100000000000000.B"
      mem200tb: "memory = 200000000000000.B"
      mem500tb: "memory = 500000000000000.B"
      mem1gib: "memory = 1073741824.B"
      mem2gib: "memory = 2147483648.B"
      mem4gib: "memory = 4294967296.B"
      mem8gib: "memory = 8589934592.B"
      mem16gib: "memory = 17179869184.B"
      mem32gib: "memory = 34359738368.B"
      mem64gib: "memory = 68719476736.B"
      mem128gib: "memory = 137438953472.B"
      mem256gib: "memory = 274877906944.B"
      mem512gib: "memory = 549755813888.B"
      mem1tib: "memory = 1099511627776.B"
      mem2tib: "memory = 2199023255552.B"
      mem4tib: "memory = 4398046511104.B"
      mem8tib: "memory = 8796093022208.B"
      mem16tib: "memory = 17592186044416.B"
      mem32tib: "memory = 35184372088832.B"
      mem64tib: "memory = 70368744177664.B"
      mem128tib: "memory = 140737488355328.B"
      mem256tib: "memory = 281474976710656.B"
      mem512tib: "memory = 562949953421312.B"
      cpu1: "cpus = 1"
      cpu2: "cpus = 2"
      cpu5: "cpus = 5"
      cpu10: "cpus = 10"
      cpu20: "cpus = 20"
      cpu50: "cpus = 50"
      cpu100: "cpus = 100"
      cpu200: "cpus = 200"
      cpu500: "cpus = 500"
      cpu1000: "cpus = 1000"
    script:
    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
engines:
- type: "docker"
  id: "docker"
  image: "debian:latest"
  target_registry: "images.viash-hub.com"
  target_tag: "v4.0.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
    packages:
    - "freebayes"
    interactive: false
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/genetic_demux/freebayes/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/genetic_demux/freebayes"
  executable: "target/executable/genetic_demux/freebayes/freebayes"
  viash_version: "0.9.4"
  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
  git_remote: "https://github.com/openpipelines-bio/openpipeline"
package_config:
  name: "openpipeline"
  version: "v4.0.1"
  summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
  description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
    \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
    \nIn terms of workflows, the following has been made available, but keep in mind\
    \ that\nindividual tools and functionality can be executed as standalone components\
    \ as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n\
    \  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample\
    \ processing: cell filtering and doublet detection.\n  * Multisample processing:\
    \ Count transformation, normalization, QC metric calulations.\n  * Integration:\
    \ Clustering, integration and batch correction using single and multimodal methods.\n\
    \  * Downstream analysis workflows\n"
  info:
    test_resources:
    - type: "s3"
      path: "s3://openpipelines-data"
      dest: "resources_test"
    nextflow_labels_ci:
    - path: "src/workflows/utils/labels_ci.config"
      description: "Adds the correct memory and CPU labels when running on the Viash\
        \ Hub CI."
  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
  - ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
    )'"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
  keywords:
  - "single-cell"
  - "multimodal"
  license: "MIT"
  organization: "vsh"
  links:
    repository: "https://github.com/openpipelines-bio/openpipeline"
    docker_registry: "ghcr.io"
    homepage: "https://openpipelines.bio"
    documentation: "https://openpipelines.bio/fundamentals"
    issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
