name: "deseq2_qc"
version: "main"
argument_groups:
- name: "Input"
  arguments:
  - type: "file"
    name: "--counts"
    description: "Count file matrix where rows are genes and columns are samples"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--pca_header_multiqc"
    info: null
    default:
    - "assets/multiqc/deseq2_pca_header.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--clustering_header_multiqc"
    info: null
    default:
    - "assets/multiqc/deseq2_clustering_header.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--deseq2_vst"
    description: "Use vst transformation instead of rlog with DESeq2"
    info: null
    default:
    - true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--extra_args"
    info: null
    default:
    - "--id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--extra_args2"
    info: null
    default:
    - "star_salmon"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Output"
  arguments:
  - type: "file"
    name: "--deseq2_output"
    info: null
    default:
    - "deseq2"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--pca_multiqc"
    info: null
    default:
    - "deseq2.pca.vals_mqc.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--dists_multiqc"
    info: null
    default:
    - "deseq2.sample.dists_mqc.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
- type: "file"
  path: "deseq2_qc.r"
description: "Run DESeq2, perform PCA, generate heatmaps and scatterplots for samples\
  \ in the counts files\n"
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
- type: "file"
  path: "counts.tsv"
- type: "file"
  path: "deseq2_pca_header.txt"
- type: "file"
  path: "deseq2_clustering_header.txt"
info:
  migration_info:
    git_repo: "https://github.com/nf-core/rnaseq.git"
    paths:
    - "modules/local/deseq2_qc.nf"
    last_sha: "92b2a7857de1dda9d1c19a088941fc81e2976ff7"
status: "enabled"
requirements:
  commands:
  - "ps"
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:
    - "r-base"
    - "libcurl4-openssl-dev"
    - "libssl-dev"
    - "libxml2-dev"
    interactive: false
  - type: "r"
    cran:
    - "optparse"
    - "ggplot2"
    - "RColorBrewer"
    - "pheatmap"
    bioc:
    - "DESeq2"
    url:
    - "https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"
    bioc_force_install: false
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/deseq2_qc/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/deseq2_qc"
  executable: "target/executable/deseq2_qc/deseq2_qc"
  viash_version: "0.9.0"
  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
  git_remote: "https://github.com/viash-hub/rnaseq"
package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
  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"