rnaseq/target/executable/workflows/merge_quant_results/.config.vsh.yaml

name: "merge_quant_results"
namespace: "workflows"
version: "main"
argument_groups:
- name: "Input"
  arguments:
  - type: "file"
    name: "--salmon_quant_results"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ","
  - type: "file"
    name: "--kallisto_quant_results"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ","
  - type: "file"
    name: "--gtf"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--gtf_extra_attributes"
    info: null
    default:
    - "gene_name"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--gtf_group_features"
    info: null
    default:
    - "gene_id"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--quant_type"
    description: "Quantification method used."
    info: null
    default:
    - "salmon"
    required: false
    choices:
    - "salmon"
    - "kallisto"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--versions"
    info: null
    must_exist: false
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Output"
  arguments:
  - type: "file"
    name: "--tpm_gene"
    info: null
    example:
    - "gene_tpm.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--counts_gene"
    info: null
    example:
    - "gene_counts.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--counts_gene_length_scaled"
    info: null
    example:
    - "gene_counts_length_scaled.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--counts_gene_scaled"
    info: null
    example:
    - "gene_counts_scaled.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--tpm_transcript"
    info: null
    example:
    - "transcript_tpm.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--lengths_gene"
    info: null
    example:
    - "gene_length.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--counts_transcript"
    info: null
    example:
    - "transcript_counts.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--lengths_transcript"
    info: null
    example:
    - "transcript_length.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--quant_merged_summarizedexperiment"
    info: null
    example:
    - "quant_merged_summarizedexperiment"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
resources:
- type: "nextflow_script"
  path: "main.nf"
  is_executable: true
  entrypoint: "run_wf"
- type: "file"
  path: "nextflow_labels.config"
  dest: "nextflow_labels.config"
description: "A sub-workflow to merge the counts obtained from salmon quant across\
  \ all samples."
info: null
status: "enabled"
requirements:
  commands:
  - "ps"
dependencies:
- name: "tx2gene"
  repository:
    type: "local"
- name: "tximport"
  repository:
    type: "local"
- name: "summarizedexperiment"
  repository:
    type: "local"
repositories:
- type: "vsh"
  name: "biobox"
  repo: "biobox"
  tag: "main"
- 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"
    script:
    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
engines:
- type: "native"
  id: "native"
build_info:
  config: "src/workflows/merge_quant_results/config.vsh.yaml"
  runner: "executable"
  engine: "native"
  output: "target/executable/workflows/merge_quant_results"
  executable: "target/executable/workflows/merge_quant_results/merge_quant_results"
  viash_version: "0.9.0"
  git_commit: "2b3d511b34246648b934fd1dc99b22e0a71c37f2"
  git_remote: "https://x-access-token:ghs_mpjpezoXRPhvITbEzvFPaxzcp8yfML2ITu9P@github.com/viash-hub/rnaseq"
  dependencies:
  - "target/nextflow/tx2gene"
  - "target/nextflow/tximport"
  - "target/nextflow/summarizedexperiment"
package_config:
  name: "rnaseq"
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
  repositories:
  - type: "vsh"
    name: "biobox"
    repo: "biobox"
    tag: "main"
  - 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.resources += {path: '/src/workflows/utils/labels.config',\
    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
    \ := '$id'\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'main'"
  organization: "vsh"