name: "quality_control"
namespace: "workflows"
version: "add_biobase_modules"
argument_groups:
- name: "Input"
  arguments:
  - type: "string"
    name: "--id"
    description: "ID of the sample"
    info: null
    example:
    - "test"
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--strandedness"
    description: "Sample strand-specificity. Must be one of unstranded, forward, reverse"
    info: null
    default:
    - "unstranded"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--paired"
    description: "Paired-end reads?"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--genome_bam"
    description: "Input genome BAM file"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--genome_bam_index"
    description: "Genome BAM index file"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--gene_bed"
    description: "Path to BED file containing gene intervals. This will be created\
      \ from the GTF file if not specified."
    info: null
    must_exist: true
    create_parent: true
    required: false
    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: "string"
    name: "--gtf_group_features"
    description: "Define the attribute type used to group features in the GTF file\
      \ when running Salmon."
    info: null
    default:
    - "gene_id"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--gtf_extra_attributes"
    description: "By default, the pipeline uses the gene_name field to obtain additional\
      \ gene identifiers from the input GTF file when running Salmon."
    info: null
    default:
    - "gene_name"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--quant_out_dir"
    description: "Directory containing quantification results."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--quant_results_file"
    description: "Quantification file."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--pseudo_quant_out_dir"
    description: "Directory containing quantification results for pseudo alignment."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--pseudo_salmon_quant_results_file"
    description: "Quantification file from Salmon for pseudo alignment."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--pseudo_kallisto_quant_results_file"
    description: "Quantification file from Kallisto for pseudo alignment."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--aligner"
    description: "Method used for alognment and qqunatification."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--pseudo_aligner"
    description: "Method used for [seudo alignment and quantification."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--skip_qc"
    info: null
    default:
    - false
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--skip_biotype_qc"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--skip_align"
    info: null
    default:
    - false
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--skip_pseudo_align"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--skip_preseq"
    info: null
    default:
    - false
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--extra_preseq_args"
    info: null
    default:
    - "-verbose -bam -seed 1"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--featurecounts_group_type"
    description: "The attribute type used to group feature types in the GTF file when\
      \ generating the biotype plot with featureCounts."
    info: null
    default:
    - "gene_biotype"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--featurecounts_feature_type"
    description: "By default, the pipeline assigns reads based on the 'exon' attribute\
      \ within the GTF file."
    info: null
    default:
    - "exon"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--gencode"
    description: "Specify if the GTF annotation is in GENCODE format."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--biotypes_header"
    info: null
    default:
    - "assets/multiqc/biotypes_header.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--biotype"
    description: "Biotype value to use while appending entries to GTF file when additional\
      \ fasta file is provided."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--extra_featurecounts_args"
    description: "Extra arguments to pass to featureCounts command in addition to\
      \ defaults defined by the pipeline"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--rseqc_modules"
    description: "Specify the RSeQC modules to run_wf"
    info: null
    default:
    - "bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication"
    required: false
    choices:
    - "bam_stat"
    - "inner_distance"
    - "infer_experiment"
    - "junction_annotation"
    - "junction_saturation"
    - "read_distribution"
    - "read_duplication"
    - "tin"
    direction: "input"
    multiple: true
    multiple_sep: ","
  - type: "integer"
    name: "--sample_size"
    description: "Numer of reads sampled from SAM/BAM file to infer experiment and\
      \ calculate inner distance, default = 200000."
    info: null
    default:
    - 200000
    required: false
    min: 1
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--lower_bound_size"
    description: "Lower bound of inner distance (bp). This option is used for ploting\
      \ histograme, default = -250."
    info: null
    default:
    - -250
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--upper_bound_size"
    description: "Upper bound of inner distance (bp). This option is used for ploting\
      \ histograme, default = 250."
    info: null
    default:
    - 250
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--step_size"
    description: "Step size (bp) of histograme of inner distance. This option is used\
      \ for plotting histogram, default = 5."
    info: null
    default:
    - 5
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--map_qual"
    description: "Minimum mapping quality (phred scaled) to determine uniquely mapped\
      \ reads, default = 30."
    info: null
    default:
    - 30
    required: false
    min: 0
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--min_intron"
    description: "Minimum intron length (bp) to call a junction, default = 50."
    info: null
    default:
    - 50
    required: false
    min: 1
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--min_splice_read"
    description: "Minimum number of supporting reads to call a junction, default =\
      \ 1."
    info: null
    default:
    - 1
    required: false
    min: 1
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--sampling_percentile_lower_bound"
    description: "Read sampling for junction saturation starts from this percentile,\
      \ must be an integer between 0 and 100, default = 5."
    info: null
    default:
    - 5
    required: false
    min: 0
    max: 100
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--sampling_percentile_upper_bound"
    description: "Read sampling for junction saturation ends at this percentile, must\
      \ be an integer between 0 and 100, default = 5."
    info: null
    default:
    - 100
    required: false
    min: 0
    max: 100
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--sampling_percentile_step"
    description: "Read sampling for junction saturation frequency in %. Smaller value\
      \ means more sampling times. Must be an integer between 0 and 100, default =\
      \ 5."
    info: null
    default:
    - 5
    required: false
    min: 0
    max: 100
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--read_count_upper_limit"
    description: "Upper limit of reads' occurence to determine read duplication. Only\
      \ used for plotting, default = 500 (times)."
    info: null
    default:
    - 500
    required: false
    min: 1
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--minimum_coverage"
    description: "Minimum number of reads mapped to a transcript to determin tin,\
      \ default = 10."
    info: null
    default:
    - 10
    required: false
    min: 1
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--tin_sample_size"
    description: "Number of equal-spaced nucleotide positions picked from mRNA. Note,\
      \ if this number is larger than the length of mRNA (L), it will be halved until\
      \ it's smaller than L (default = 100)"
    info: null
    default:
    - 100
    required: false
    min: 1
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--subtract_background"
    description: "Set flag to subtract background noise (estimated from intronic reads)\
      \ to determine tin. Only use this option if there are substantial intronic reads."
    info: null
    direction: "input"
  - type: "string"
    name: "--output_format"
    description: "Format of the qualimap output report (PDF or HTML, default is HTML)"
    info: null
    default:
    - "html"
    required: false
    choices:
    - "html"
    - "pdf"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--pr_bases"
    description: "Number of upstream/downstream nucleotide bases to compute 5'-3'\
      \ bias for qualimap (default = 100)."
    info: null
    default:
    - 100
    required: false
    min: 1
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--tr_bias"
    description: "Number of top highly expressed transcripts to compute 5'-3' bias\
      \ for qualimap (default = 1000)."
    info: null
    default:
    - 1000
    required: false
    min: 1
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--algorithm"
    description: "Counting algorithm for qualimap (uniquely-mapped-reads (default)\
      \ or proportional)."
    info: null
    default:
    - "uniquely-mapped-reads"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--sequencing_protocol"
    description: "Sequencing library protocol for qualimap (strand-specific-forward,\
      \ strand-specific-reverse or non-strand-specific (default))."
    info: null
    default:
    - "non-strand-specific"
    required: false
    choices:
    - "non-strand-specific"
    - "strand-specific-reverse"
    - "strand-specific-forward"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - 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\
      \ for qualimap. Only requiredfor paired-end analysis."
    info: null
    direction: "input"
  - type: "string"
    name: "--java_memory_size"
    description: "maximum Java heap memory size for qualimap, default = 4G."
    info: null
    default:
    - "4G"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--skip_deseq2_qc"
    info: null
    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
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--extra_deseq2_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_deseq2_args2"
    info: null
    default:
    - "star_salmon"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--multiqc_custom_config"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--multiqc_title"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--multiqc_methods_description"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--mqc_yml"
    description: "Software versions"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--workflow_summary"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--passed_trimmed_reads"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "double"
    name: "--num_trimmed_reads"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--passed_mapping"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "double"
    name: "--percent_mapped"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--fastqc_zip_1"
    info: null
    must_exist: false
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--fastqc_zip_2"
    info: null
    must_exist: false
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--trim_zip_1"
    info: null
    must_exist: false
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--trim_zip_2"
    info: null
    must_exist: false
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--trim_log_1"
    info: null
    must_exist: false
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--trim_log_2"
    info: null
    must_exist: false
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--sortmerna_multiqc"
    info: null
    must_exist: false
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--star_multiqc"
    info: null
    must_exist: false
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--genome_bam_stats"
    info: null
    must_exist: false
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--genome_bam_flagstat"
    info: null
    must_exist: false
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--genome_bam_idxstats"
    info: null
    must_exist: false
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--markduplicates_multiqc"
    info: null
    must_exist: false
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--pseudo_multiqc"
    info: null
    must_exist: false
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Output"
  arguments:
  - type: "file"
    name: "--preseq_output"
    info: null
    default:
    - "$id.lc_extrap.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bamstat_output"
    description: "Path to output file (txt) of mapping quality statistics"
    info: null
    default:
    - "$id.mapping_quality.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--strandedness_output"
    description: "Path to output report (txt) of inferred strandedness"
    info: null
    default:
    - "$id.strandedness.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--inner_dist_output_stats"
    description: "output file (txt) with summary statistics of inner distances of\
      \ paired reads"
    info: null
    default:
    - "$id.inner_distance.stats"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--inner_dist_output_dist"
    description: "output file (txt) with inner distances of all paired reads"
    info: null
    default:
    - "$id.inner_distance.txt"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--inner_dist_output_freq"
    description: "output file (txt) with frequencies of inner distances of all paired\
      \ reads"
    info: null
    default:
    - "$id.inner_distance_freq.txt"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--inner_dist_output_plot"
    description: "output file (pdf) with histogram plot of of inner distances of all\
      \ paired reads"
    info: null
    default:
    - "$id.inner_distance_plot.pdf"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--inner_dist_output_plot_r"
    description: "output file (R) with script of histogram plot of of inner distances\
      \ of all paired reads"
    info: null
    default:
    - "$id.inner_distance_plot.r"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--junction_annotation_output_log"
    description: "output log of junction annotation script"
    info: null
    default:
    - "$id.junction_annotation.log"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--junction_annotation_output_plot_r"
    description: "R script to generate splice_junction and splice_events plot"
    info: null
    default:
    - "$id.junction_annotation_plot.r"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--junction_annotation_output_junction_bed"
    description: "junction annotation file (bed format)"
    info: null
    default:
    - "$id.junction_annotation.bed"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--junction_annotation_output_junction_interact"
    description: "interact file (bed format) of junctions. Can be uploaded to UCSC\
      \ genome browser or converted to bigInteract (using bedToBigBed program) for\
      \ visualization."
    info: null
    default:
    - "$id.junction_annotation.Interact.bed"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--junction_annotation_output_junction_sheet"
    description: "junction annotation file (xls format)"
    info: null
    default:
    - "$id.junction_annotation.xls"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--junction_annotation_output_splice_events_plot"
    description: "plot of splice events (pdf)"
    info: null
    default:
    - "$id.splice_events.pdf"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--junction_annotation_output_splice_junctions_plot"
    description: "plot of junctions (pdf)"
    info: null
    default:
    - "$id.splice_junctions_plot.pdf"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--junction_saturation_output_plot_r"
    description: "r script to generate junction_saturation_plot plot"
    info: null
    default:
    - "$id.junction_saturation_plot.r"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--junction_saturation_output_plot"
    description: "plot of junction saturation (pdf"
    info: null
    default:
    - "$id.junction_saturation_plot.pdf"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--read_distribution_output"
    description: "output file (txt) of read distribution analysis."
    info: null
    default:
    - "$id.read_distribution.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--read_duplication_output_duplication_rate_plot_r"
    description: "R script for generating duplication rate plot"
    info: null
    default:
    - "$id.duplication_rate_plot.r"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--read_duplication_output_duplication_rate_plot"
    description: "duplication rate plot (pdf)"
    info: null
    default:
    - "$id.duplication_rate_plot.pdf"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--read_duplication_output_duplication_rate_mapping"
    description: "Summary of mapping-based read duplication"
    info: null
    default:
    - "$id.duplication_rate_mapping.xls"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--read_duplication_output_duplication_rate_sequence"
    description: "Summary of sequencing-based read duplication"
    info: null
    default:
    - "$id.duplication_rate_sequencing.xls"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--tin_output_summary"
    description: "summary statistics (txt) of calculated TIN metrics"
    info: null
    default:
    - "$id.tin_summary.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--tin_output_metrics"
    description: "file with TIN metrics (xls)"
    info: null
    default:
    - "$id.tin.xls"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--dupradar_output_dupmatrix"
    description: "path to output file (txt) of duplicate tag counts"
    info: null
    default:
    - "$id.dup_matrix.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--dupradar_output_dup_intercept_mqc"
    description: "path to output file (txt) of multiqc intercept value DupRadar"
    info: null
    default:
    - "$id.dup_intercept_mqc.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--dupradar_output_duprate_exp_boxplot"
    description: "path to output file (pdf) of distribution of expression box plot"
    info: null
    default:
    - "$id.duprate_exp_boxplot.pdf"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--dupradar_output_duprate_exp_densplot"
    description: "path to output file (pdf) of 2D density scatter plot of duplicate\
      \ tag counts"
    info: null
    default:
    - "$id.duprate_exp_densityplot.pdf"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--dupradar_output_duprate_exp_denscurve_mqc"
    description: "path to output file (pdf) of density curve of gene duplication multiqc"
    info: null
    default:
    - "$id.duprate_exp_density_curve_mqc.pdf"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--dupradar_output_expression_histogram"
    description: "path to output file (pdf) of distribution of RPK values per gene\
      \ histogram"
    info: null
    default:
    - "$id.expression_hist.pdf"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--dupradar_output_intercept_slope"
    info: null
    default:
    - "$id.intercept_slope.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--qualimap_output_pdf"
    info: null
    default:
    - "$id.qualimap_output.pdf"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--qualimap_output_dir"
    info: null
    default:
    - "$id.qualimap_output"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--deseq2_output"
    info: null
    default:
    - "deseq2"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--deseq2_output_pseudo"
    info: null
    default:
    - "deseq2_pseudo"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--multiqc_report"
    info: null
    default:
    - "multiqc_report.html"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--multiqc_data"
    info: null
    default:
    - "multiqc_data"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--multiqc_plots"
    info: null
    default:
    - "multiqc_plots"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--multiqc_versions"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--featurecounts"
    info: null
    default:
    - "$id.featureCounts.txt"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--featurecounts_summary"
    info: null
    default:
    - "$id.featureCounts.txt.summary"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--featurecounts_multiqc"
    info: null
    default:
    - "$id.featureCounts_mqc.tsv"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--featurecounts_rrna_multiqc"
    info: null
    default:
    - "$id.featureCounts_rrna_mqc.tsv"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--tpm_gene"
    info: null
    default:
    - "salmon.merged.gene_tpm.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--counts_gene"
    info: null
    default:
    - "salmon.merged.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
    default:
    - "salmon.merged.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
    default:
    - "salmon.merged.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
    default:
    - "salmon.merged.transcript_tpm.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--counts_transcript"
    info: null
    default:
    - "salmon.merged.transcript_counts.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--quant_merged_summarizedexperiment"
    info: null
    default:
    - "salmon_merged_summarizedexperiment"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--pseudo_tpm_gene"
    info: null
    default:
    - "salmon.merged.pseudo_gene_tpm.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--pseudo_counts_gene"
    info: null
    default:
    - "salmon.merged.pseudo_gene_counts.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--pseudo_counts_gene_length_scaled"
    info: null
    default:
    - "salmon.merged.pseudo_gene_counts_length_scaled.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--pseudo_counts_gene_scaled"
    info: null
    default:
    - "salmon.merged.pseudo_gene_counts_scaled.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--pseudo_tpm_transcript"
    info: null
    default:
    - "salmon.merged.pseudo_transcript_tpm.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--pseudo_counts_transcript"
    info: null
    default:
    - "salmon.merged.pseudo_transcript_counts.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--pseudo_quant_merged_summarizedexperiment"
    info: null
    default:
    - "pseudo_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"
description: "A subworkflow for the final quality control stage of the nf-core/rnaseq\
  \ pipeline.\n"
info: null
status: "enabled"
requirements:
  commands:
  - "ps"
dependencies:
- name: "rseqc/rseqc_bamstat"
  repository:
    type: "local"
- name: "rseqc/rseqc_inferexperiment"
  repository:
    type: "local"
- name: "rseqc/rseqc_innerdistance"
  repository:
    type: "local"
- name: "rseqc/rseqc_junctionannotation"
  repository:
    type: "local"
- name: "rseqc/rseqc_junctionsaturation"
  repository:
    type: "local"
- name: "rseqc/rseqc_readdistribution"
  repository:
    type: "local"
- name: "rseqc/rseqc_readduplication"
  repository:
    type: "local"
- name: "rseqc/rseqc_tin"
  repository:
    type: "local"
- name: "dupradar"
  repository:
    type: "local"
- name: "qualimap"
  repository:
    type: "local"
- name: "preseq_lcextrap"
  repository:
    type: "local"
- name: "featurecounts"
  repository:
    type: "vsh"
    repo: "vsh/biobox"
    tag: "v0.1"
- name: "multiqc_custom_biotype"
  repository:
    type: "local"
- name: "deseq2_qc"
  repository:
    type: "local"
- name: "prepare_multiqc_input"
  repository:
    type: "local"
- name: "multiqc"
  repository:
    type: "vsh"
    repo: "vsh/biobox"
    tag: "v0.1"
- name: "workflows/merge_quant_results"
  repository:
    type: "local"
repositories:
- type: "vsh"
  name: "biobox"
  repo: "vsh/biobox"
  tag: "v0.1"
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/quality_control/config.vsh.yaml"
  runner: "executable"
  engine: "native"
  output: "target/executable/workflows/quality_control"
  executable: "target/executable/workflows/quality_control/quality_control"
  viash_version: "0.9.0"
  git_commit: "b0cbbf82c331a079e3d5ad6df5c8b56388349cac"
  git_remote: "https://github.com/viash-hub/rnaseq"
  dependencies:
  - "target/nextflow/rseqc/rseqc_bamstat"
  - "target/nextflow/rseqc/rseqc_inferexperiment"
  - "target/nextflow/rseqc/rseqc_innerdistance"
  - "target/nextflow/rseqc/rseqc_junctionannotation"
  - "target/nextflow/rseqc/rseqc_junctionsaturation"
  - "target/nextflow/rseqc/rseqc_readdistribution"
  - "target/nextflow/rseqc/rseqc_readduplication"
  - "target/nextflow/rseqc/rseqc_tin"
  - "target/nextflow/dupradar"
  - "target/nextflow/qualimap"
  - "target/nextflow/preseq_lcextrap"
  - "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/featurecounts"
  - "target/nextflow/multiqc_custom_biotype"
  - "target/nextflow/deseq2_qc"
  - "target/nextflow/prepare_multiqc_input"
  - "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/multiqc"
  - "target/nextflow/workflows/merge_quant_results"
package_config:
  version: "add_biobase_modules"
  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 := 'add_biobase_modules'"
  organization: "vsh"
