name: "qualimap_rnaseq"
namespace: "qualimap"
version: "add_sgdemux"
authors:
- name: "Dorien Roosen"
  roles:
  - "author"
  - "maintainer"
  info:
    links:
      email: "dorien@data-intuitive.com"
      github: "dorien-er"
      linkedin: "dorien-roosen"
    organizations:
    - name: "Data Intuitive"
      href: "https://www.data-intuitive.com"
      role: "Data Scientist"
argument_groups:
- name: "Input"
  arguments:
  - type: "file"
    name: "--bam"
    description: "Path to the sequence alignment file in BAM format, produced by a\
      \ splicing-aware aligner."
    info: null
    example:
    - "alignment.bam"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--gtf"
    description: "Path to genomic annotations in Ensembl GTF format."
    info: null
    example:
    - "annotations.gtf"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Output"
  arguments:
  - type: "file"
    name: "--qc_results"
    description: "Text file containing the RNAseq QC results."
    info: null
    example:
    - "rnaseq_qc_results.txt"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--counts"
    description: "Output file for computed counts."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--report"
    description: "Report output file. Supported formats are PDF or HTML."
    info: null
    example:
    - "report.html"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Optional"
  arguments:
  - type: "integer"
    name: "--num_pr_bases"
    description: "Number of upstream/downstream nucleotide bases to compute 5'-3'\
      \ bias (default = 100)."
    info: null
    required: false
    min: 1
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--num_tr_bias"
    description: "Number of top highly expressed transcripts to compute 5'-3' bias\
      \ (default = 1000)."
    info: null
    required: false
    min: 1
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--algorithm"
    description: "Counting algorithm (uniquely-mapped-reads (default) or proportional)."
    info: null
    required: false
    choices:
    - "uniquely-mapped-reads"
    - "proportional"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--sequencing_protocol"
    description: "Sequencing library protocol (strand-specific-forward, strand-specific-reverse\
      \ or non-strand-specific (default))."
    info: null
    required: false
    choices:
    - "non-strand-specific"
    - "strand-specific-reverse"
    - "strand-specific-forward"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--paired"
    description: "Setting this flag for paired-end experiments will result in counting\
      \ fragments instead of reads."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--sorted"
    description: "Setting this flag indicates that the input file is already sorted\
      \ by name. If flag is not set, additional sorting by name will be performed.\
      \ Only requiredfor paired-end analysis."
    info: null
    direction: "input"
  - type: "string"
    name: "--java_memory_size"
    description: "maximum Java heap memory size, default = 4G."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Qualimap RNA-seq QC reports quality control metrics and bias estimations\
  \ \nwhich are specific for whole transcriptome sequencing, including reads genomic\
  \ \norigin, junction analysis, transcript coverage and 5’-3’ bias computation.\n"
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
- type: "file"
  path: "test_data"
info: null
status: "enabled"
requirements:
  commands:
  - "ps"
keywords:
- "RNA-seq"
- "quality control"
- "QC Report"
license: "GPL-2.0"
references:
  doi:
  - "10.1093/bioinformatics/btv566"
links:
  repository: "https://bitbucket.org/kokonech/qualimap/commits/branch/master"
  homepage: "http://qualimap.conesalab.org/"
  documentation: "http://qualimap.conesalab.org/doc_html/analysis.html#rna-seq-qc"
  issue_tracker: "https://bitbucket.org/kokonech/qualimap/issues?status=new&status=open"
runners:
- type: "executable"
  id: "executable"
  docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
  id: "nextflow"
  directives:
    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"
  debug: false
  container: "docker"
engines:
- type: "docker"
  id: "docker"
  image: "quay.io/biocontainers/qualimap:2.3--hdfd78af_0"
  target_registry: "images.viash-hub.com"
  target_tag: "add_sgdemux"
  namespace_separator: "/"
  setup:
  - type: "docker"
    run:
    - "echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/qualimap/qualimap_rnaseq/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/qualimap/qualimap_rnaseq"
  executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq"
  viash_version: "0.9.0"
  git_commit: "402ad6a813c0d0b141bbf8f9a3aab9c270a74812"
  git_remote: "https://x-access-token:ghs_VWGBwCOTHxXRJ07uVE94xFn8UJ2FmS0FLhmc@github.com/viash-hub/biobox"
  git_tag: "v0.2.0-27-g402ad6a"
package_config:
  name: "biobox"
  version: "add_sgdemux"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'add_sgdemux'"
  keywords:
  - "bioinformatics"
  - "modules"
  - "sequencing"
  license: "MIT"
  organization: "vsh"
  links:
    repository: "https://github.com/viash-hub/biobox"
    issue_tracker: "https://github.com/viash-hub/biobox/issues"
