name: "rsem_calculate_expression"
namespace: "rsem"
version: "main"
argument_groups:
- name: "Input"
  arguments:
  - type: "string"
    name: "--id"
    description: "Sample ID."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--strandedness"
    description: "Sample strand-specificity. Must be one of unstranded, forward, reverse"
    info: null
    required: false
    choices:
    - "forward"
    - "reverse"
    - "unstranded"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--paired"
    description: "Paired-end reads or not?"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--input"
    description: "Input reads for quantification."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ","
  - type: "file"
    name: "--index"
    description: "RSEM index."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--extra_args"
    description: "Extra rsem-calculate-expression arguments in addition to the defaults."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Output"
  arguments:
  - type: "file"
    name: "--counts_gene"
    description: "Expression counts on gene level"
    info: null
    example:
    - "sample.genes.results"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--counts_transcripts"
    description: "Expression counts on transcript level"
    info: null
    example:
    - "sample.isoforms.results"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--stat"
    description: "RSEM statistics"
    info: null
    example:
    - "sample.stat"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--logs"
    description: "RSEM logs"
    info: null
    example:
    - "sample.log"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bam_star"
    description: "BAM file generated by STAR (optional)"
    info: null
    example:
    - "sample.STAR.genome.bam"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bam_genome"
    description: "Genome BAM file (optional)"
    info: null
    example:
    - "sample.genome.bam"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bam_transcript"
    description: "Transcript BAM file (optional)"
    info: null
    example:
    - "sample.transcript.bam"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Calculate expression with RSEM.\n"
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
- type: "file"
  path: "SRR6357070_1.fastq.gz"
- type: "file"
  path: "SRR6357070_2.fastq.gz"
- type: "file"
  path: "rsem.tar.gz"
info:
  migration_info:
    git_repo: "https://github.com/nf-core/rnaseq.git"
    paths:
    - "modules/nf-core/rsem/calculateexpression/main.nf"
    - "modules/nf-core/rsem/calculateexpression/meta.yml"
    last_sha: "92b2a7857de1dda9d1c19a088941fc81e2976ff7"
status: "enabled"
requirements:
  commands:
  - "ps"
repositories:
- type: "vsh"
  name: "biobox"
  repo: "vsh/biobox"
  tag: "v0.2.0"
- type: "vsh"
  name: "craftbox"
  repo: "craftbox"
  tag: "v0.1.0"
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: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
  target_tag: "main"
  namespace_separator: "/"
  setup:
  - type: "apt"
    packages:
    - "build-essential"
    - "gcc"
    - "g++"
    - "make"
    - "wget"
    - "zlib1g-dev"
    - "unzip"
    - "xxd"
    - "perl"
    - "r-base"
    - "bowtie2"
    - "python3-pip"
    - "git"
    interactive: false
  - type: "docker"
    run:
    - "ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone\
      \ && \\\ncd /tmp && \\\nwget --no-check-certificate https://github.com/alexdobin/STAR/archive/refs/tags/${STAR_VERSION}.zip\
      \ && \\\nunzip ${STAR_VERSION}.zip && \\\ncd STAR-${STAR_VERSION}/source &&\
      \ \\\nmake STARstatic CXXFLAGS_SIMD=-std=c++11 && \\\ncp STAR /usr/local/bin\
      \ && \\\ncd /tmp && \\\nwget --no-check-certificate https://github.com/deweylab/RSEM/archive/refs/tags/v${RSEM_VERSION}.zip\
      \ && \\\nunzip v${RSEM_VERSION}.zip && \\\ncd RSEM-${RSEM_VERSION} && \\\nmake\
      \ && \\\nmake install && \\\nrm -rf /tmp/STAR-${STAR_VERSION} /tmp/${STAR_VERSION}.zip\
      \ && \\\nrm -rf /tmp/RSEM-${RSEM_VERSION} /tmp/v${RSEM_VERSION}.zip && \\\n\
      cd && \\\napt-get clean && \\\necho 'export PATH=$PATH:/usr/local/bin' >> /etc/profile\
      \ && \\\necho 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \\\n/bin/bash\
      \ -c \"source /etc/profile && source ~/.bashrc && echo $PATH && which STAR\"\
      \n"
    env:
    - "STAR_VERSION=2.7.11b"
    - "RSEM_VERSION=1.3.3"
    - "TZ=Europe/Brussels"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/rsem/rsem_calculate_expression/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/rsem/rsem_calculate_expression"
  executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression"
  viash_version: "0.9.0"
  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
  repositories:
  - type: "vsh"
    name: "biobox"
    repo: "vsh/biobox"
    tag: "v0.2.0"
  - type: "vsh"
    name: "craftbox"
    repo: "craftbox"
    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'main'"
  organization: "vsh"