name: "post_processing"
namespace: "workflows"
version: "bugfix"
argument_groups:
- name: "Input"
  arguments:
  - type: "string"
    name: "--id"
    description: "ID of the sample."
    info: null
    example:
    - "foo"
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--strandedness"
    description: "Sample strand-specificity. Must be one of unstranded, forward, reverse\
      \ or auto"
    info: null
    default:
    - "auto"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--paired"
    description: "Paired fastq files or not?"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--fasta"
    description: "Path to FASTA genome file."
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--fai"
    description: "Path to FASTA index"
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--gtf"
    description: "GTF file"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--genome_bam"
    description: "Genome BAM file"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--chrom_sizes"
    description: "File containing chromosome lengths"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--star_multiqc"
    description: "STAR align log file."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--extra_picard_args"
    description: "Extra arguments to pass to picard MarkDuplicates command in addition\
      \ to defaults defined by the pipeline."
    info: null
    default:
    - ""
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--extra_stringtie_args"
    description: "Extra arguments to pass to stringtie command in addition to defaults\
      \ defined by the pipeline."
    info: null
    default:
    - ""
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--stringtie_ignore_gtf"
    description: "Perform reference-guided de novo assembly of transcripts using StringTie,\
      \ i.e. don't restrict to those in GTF file."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--extra_bedtools_args"
    description: "Extra arguments to pass to bedtools genomecov command in addition\
      \ to defaults defined by the pipeline."
    info: null
    default:
    - ""
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--bam_csi_index"
    description: "Create a CSI index for BAM files instead of the traditional BAI\
      \ index. This will be required for genomes with larger chromosome sizes."
    info: null
    default:
    - false
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--min_mapped_reads"
    description: "Minimum percentage of uniquely mapped reads below which samples\
      \ are removed from further processing."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--with_umi"
    description: "Enable UMI-based read deduplication."
    info: null
    default:
    - false
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--skip_qc"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--skip_markduplicates"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--skip_stringtie"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--skip_bigwig"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Output"
  arguments:
  - type: "file"
    name: "--processed_genome_bam"
    info: null
    default:
    - "$id.genome.bam"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--genome_bam_index"
    info: null
    default:
    - "$id.genome.bam.bai"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--genome_bam_stats"
    info: null
    default:
    - "$id.genome.stats"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--genome_bam_flagstat"
    info: null
    default:
    - "$id.genome.flagstat"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--genome_bam_idxstats"
    info: null
    default:
    - "$id.genome.idxstats"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--markduplicates_metrics"
    info: null
    default:
    - "$id.MarkDuplicates.metrics.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--stringtie_transcript_gtf"
    info: null
    default:
    - "$id.stringtie.transcripts.gtf"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--stringtie_coverage_gtf"
    info: null
    default:
    - "$id.stringtie.coverage.gtf"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--stringtie_abundance"
    info: null
    default:
    - "$id.stringtie.gene_abundance.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--stringtie_ballgown"
    info: null
    default:
    - "$id.stringtie.ballgown"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bedgraph_forward"
    info: null
    default:
    - "$id.forward.bedgraph"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bedgraph_reverse"
    info: null
    default:
    - "$id.reverse.bedgraph"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bigwig_forward"
    info: null
    default:
    - "$id.forward.bigwig"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bigwig_reverse"
    info: null
    default:
    - "$id.reverse.bigwig"
    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"
description: "A viash sub-workflow for the post-processing stage of nf-core/rnaseq\
  \ pipeline.\n"
info: null
status: "enabled"
requirements:
  commands:
  - "ps"
dependencies:
- name: "picard_markduplicates"
  repository:
    type: "local"
- name: "samtools/samtools_sort"
  repository:
    type: "vsh"
    repo: "vsh/biobox"
    tag: "main"
- name: "samtools/samtools_index"
  repository:
    type: "vsh"
    repo: "vsh/biobox"
    tag: "main"
- name: "samtools/samtools_stats"
  repository:
    type: "vsh"
    repo: "vsh/biobox"
    tag: "main"
- name: "samtools/samtools_flagstat"
  repository:
    type: "vsh"
    repo: "vsh/biobox"
    tag: "main"
- name: "samtools/samtools_idxstats"
  repository:
    type: "vsh"
    repo: "vsh/biobox"
    tag: "main"
- name: "stringtie"
  repository:
    type: "local"
- name: "bedtools_genomecov"
  repository:
    type: "local"
- name: "ucsc/bedclip"
  repository:
    type: "local"
- name: "ucsc/bedgraphtobigwig"
  repository:
    type: "local"
repositories:
- type: "vsh"
  name: "biobox"
  repo: "vsh/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"
  debug: false
  container: "docker"
engines:
- type: "native"
  id: "native"
build_info:
  config: "src/workflows/post_processing/config.vsh.yaml"
  runner: "executable"
  engine: "native"
  output: "target/executable/workflows/post_processing"
  executable: "target/executable/workflows/post_processing/post_processing"
  viash_version: "0.9.0"
  git_commit: "7662841e2e967790170bd05b667707341d27db7b"
  git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
  dependencies:
  - "target/nextflow/picard_markduplicates"
  - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort"
  - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index"
  - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats"
  - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat"
  - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats"
  - "target/nextflow/stringtie"
  - "target/nextflow/bedtools_genomecov"
  - "target/nextflow/ucsc/bedclip"
  - "target/nextflow/ucsc/bedgraphtobigwig"
package_config:
  name: "rnaseq"
  version: "bugfix"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
  repositories:
  - type: "vsh"
    name: "biobox"
    repo: "vsh/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.runners[.type == 'nextflow'].directives.tag\
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'bugfix'"
  organization: "vsh"