name: "rnaseq"
namespace: "workflows"
version: "multiple_fixes"
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: "file"
    name: "--fastq_1"
    description: "Path to the sample (or read 1 of paired end sample)."
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--fastq_2"
    description: "Path to read 2 of the sample."
    info: null
    must_exist: false
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    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
    choices:
    - "unstranded"
    - "forward"
    - "reverse"
    - "auto"
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Reference genome options"
  arguments:
  - 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: "--gtf"
    description: "Path to GTF annotation file. This parameter is *mandatory* if --genome\
      \ is not specified."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--gff"
    description: "Path to GFF3 annotation file. Required if \"--gtf\" is not specified."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--additional_fasta"
    description: "FASTA file to concatenate to genome FASTA file e.g. containing spike-in\
      \ sequences."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--transcript_fasta"
    description: "Path to FASTA transcriptome 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: "--splicesites"
    description: "Splice sites file required for HISAT2."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--star_index"
    description: "Path to directory or tar.gz archive for pre-built STAR index."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--rsem_index"
    description: "Path to directory or tar.gz archive for pre-built RSEM index."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--salmon_index"
    description: "Path to directory or tar.gz archive for pre-built Salmon index."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--kallisto_index"
    description: "Path to directory or tar.gz archive for pre-built Kallisto index."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--gencode"
    description: "Specify if the GTF annotation is in GENCODE format."
    info: null
    direction: "input"
  - type: "string"
    name: "--gtf_extra_attributes"
    description: "Additional gene identifiers from the input GTF file when running\
      \ Salmon. More than one value can be specified separated by comma."
    info: null
    default:
    - "gene_name"
    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: "--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: ";"
- name: "Read trimming options"
  arguments:
  - type: "string"
    name: "--trimmer"
    description: "Specify the trimming tool to use."
    info: null
    default:
    - "trimgalore"
    required: false
    choices:
    - "trimgalore"
    - "fastp"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--extra_trimgalore_args"
    description: "Extra arguments to pass to Trim Galore! command in addition to defaults\
      \ defined by the pipeline."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--extra_fastp_args"
    description: "Extra arguments to pass to fastp command in addition to defaults\
      \ defined by the pipeline."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--min_trimmed_reads"
    description: "Minimum number of trimmed reads below which samples are removed\
      \ from further processing. Some downstream steps in the pipeline will fail if\
      \ this threshold is too low."
    info: null
    default:
    - 10000
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Read filtering options"
  arguments:
  - type: "file"
    name: "--bbsplit_fasta_list"
    description: "Path to comma-separated file containing a list of reference genomes\
      \ to filter reads against with BBSplit. To use BBSplit, \"--skip_bbsplit\" must\
      \ be explicitly set to \"false\". The file should contain 2 (comma separated)\
      \ columns - short name and full path to reference genome(s)"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bbsplit_index"
    description: "Path to directory or tar.gz archive for pre-built BBSplit index."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--remove_ribo_rna"
    description: "Enable the removal of reads derived from ribosomal RNA using SortMeRNA."
    info: null
    direction: "input"
  - type: "file"
    name: "--ribo_database_manifest"
    description: "Text file containing paths to fasta files (one per line) that will\
      \ be used to create the database for SortMeRNA."
    info: null
    default:
    - "assets/rrna-db-defaults.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "UMI options"
  arguments:
  - type: "boolean_true"
    name: "--with_umi"
    description: "Enable UMI-based read deduplication."
    info: null
    direction: "input"
  - type: "string"
    name: "--umitools_extract_method"
    description: "UMI pattern to use."
    info: null
    default:
    - "string"
    required: false
    choices:
    - "string"
    - "regex"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--umitools_bc_pattern"
    description: "The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the\
      \ first 6 nucleotides of the read are from the UMI."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--umitools_bc_pattern2"
    description: "The UMI barcode pattern to use if the UMI is located in read 2."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--umi_discard_read"
    description: "After UMI barcode extraction discard either R1 or R2 by setting\
      \ this parameter to 1 or 2, respectively."
    info: null
    default:
    - 0
    required: false
    choices:
    - 0
    - 1
    - 2
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--umitools_umi_separator"
    description: "The character that separates the UMI in the read name. Most likely\
      \ a colon if you skipped the extraction with UMI-tools and used other software."
    info: null
    default:
    - "_"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--umitools_grouping_method"
    description: "Method to use to determine read groups by subsuming those with similar\
      \ UMIs. All methods start by identifying the reads with the same mapping position,\
      \ but treat similar yet nonidentical UMIs differently."
    info: null
    default:
    - "directional"
    required: false
    choices:
    - "unique"
    - "percentile"
    - "cluster"
    - "adjacency"
    - "directional"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--umi_dedup_stats"
    description: "Generate output stats when running \"umi_tools dedup\"."
    info: null
    direction: "input"
- name: "Alignment options"
  arguments:
  - type: "string"
    name: "--aligner"
    description: "Specifies the alignment algorithm to use - available options are\
      \ 'star_salmon', 'star_rsem' and 'hisat2'."
    info: null
    default:
    - "star_salmon"
    required: false
    choices:
    - "star_salmon"
    - "star_rsem"
    - "hisat2"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--pseudo_aligner"
    description: "Specifies the pseudo aligner to use - available options are 'salmon'.\
      \ Runs in addition to '--aligner'."
    info: null
    default:
    - "salmon"
    required: false
    choices:
    - "salmon"
    - "kallisto"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--pseudo_aligner_kmer_size"
    description: "Kmer length passed to indexing step of pseudoaligners."
    info: null
    default:
    - 31
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--kallisto_quant_fragment_length"
    description: "For single-end mode only, the estimated average fragment length\
      \ to use for quantification with Kallisto."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--kallisto_quant_fragment_length_sd"
    description: "For single-end mode only, the estimated standard deviation of the\
      \ fragment length for quantification with Kallisto."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    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
    direction: "input"
  - type: "string"
    name: "--salmon_quant_libtype"
    description: "Override Salmon library type inferred based on strandedness defined\
      \ in meta object."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--extra_salmon_quant_args"
    description: "Extra arguments to pass to salmon quant command in addition to defaults\
      \ defined by the pipeline."
    info: null
    default:
    - "-v"
    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
    default:
    - 5
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    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
    direction: "input"
  - 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:
    - "-v"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--save_unaligned"
    description: "Where possible, save unaligned reads from either STAR, HISAT2 or\
      \ Salmon to the results directory."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--save_align_intermeds"
    description: "Save the intermediate BAM files from the alignment step."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--skip_alignment"
    description: "Skip all of the alignment-based processes within the pipeline."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--skip_pseudo_alignment"
    description: "Skip all of the pseudo-alignment-based processes within the pipeline."
    info: null
    direction: "input"
  - type: "string"
    name: "--extra_rsem_calculate_expression_args"
    description: "Extra arguments to pass to rsem-calculate-expression command in\
      \ addition to defaults defined by the pipeline."
    info: null
    default:
    - "--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed\
      \ 1"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Process skipping options"
  arguments:
  - type: "boolean"
    name: "--skip_fastqc"
    description: "Skip FatQC step."
    info: null
    default:
    - false
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--skip_trimming"
    description: "Skip the adapter trimming step."
    info: null
    default:
    - false
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--skip_bbsplit"
    description: "Skip BBSplit for removal of non-reference genome reads."
    info: null
    direction: "input"
  - type: "boolean"
    name: "--skip_umi_extract"
    description: "Skip umi_tools extract step."
    info: null
    default:
    - false
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--skip_qc"
    description: "Skip all QC steps except for MultiQC."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--skip_markduplicates"
    description: "Skip picard MarkDuplicates step."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--skip_stringtie"
    description: "Skip StringTie."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--skip_biotype_qc"
    description: "Skip additional featureCounts process for biotype QC."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--skip_bigwig"
    description: "Skip bigWig file creation."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--skip_preseq"
    description: "Skip Preseq."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--skip_deseq2_qc"
    description: "Skip DESeq2 PCA and heatmap plotting."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "skip_dupradar"
    description: "Skip dupRadar."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "skip_rseqc"
    description: "Skip RSeQC."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "skip_multiqc"
    description: "Skip MultiQC."
    info: null
    direction: "input"
- name: "Other process arguments"
  arguments:
  - type: "string"
    name: "--extra_fq_subsample_args"
    description: "Extra arguments to pass to fq subsample command in addition to defaults\
      \ defined by the pipeline."
    info: null
    default:
    - " --record-count 1000000 --seed 1"
    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:
    - " --ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT\
      \ --TMP_DIR tmp"
    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:
    - " -split -du"
    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
    default:
    - " -B -C"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--extra_preseq_args"
    description: "Extra arguments to pass to preseq lc_extrap command in addition\
      \ to defaults defined by the pipeline"
    info: null
    default:
    - "-verbose -seed 1 -seg_len 100000000"
    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_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: "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: ","
- name: "Multiqc paramenters"
  arguments:
  - type: "file"
    name: "--multiqc_custom_config"
    info: null
    default:
    - "assets/multiqc_config.yml"
    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
    default:
    - "assets/methods_description_template.yml"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Output"
  arguments:
  - type: "file"
    name: "--output_fasta"
    info: null
    default:
    - "reference/genome.fasta"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--output_gtf"
    info: null
    default:
    - "reference/gene_annotation.gtf"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--output_transcript_fasta"
    info: null
    default:
    - "reference/transcriptome.fasta"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--output_gene_bed"
    info: null
    default:
    - "reference/gene_annotation.bed"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--output_star_index"
    description: "Path to STAR index."
    info: null
    default:
    - "reference/index/STAR"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--output_salmon_index"
    description: "Path to Salmon index."
    info: null
    default:
    - "reference/index/Salmon"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--output_bbsplit_index"
    description: "Path to BBSplit index."
    info: null
    default:
    - "reference/index/BBSplit"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--output_kallisto_index"
    description: "Path to Kallisto index."
    info: null
    default:
    - "reference/index/Kallisto"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--output_fastq_1"
    description: "Path to output directory"
    info: null
    default:
    - "fastq/$id.read_1.fastq"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--output_fastq_2"
    description: "Path to output directory"
    info: null
    default:
    - "fastq/$id.read_2.fastq"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--fastqc_html_1"
    description: "FastQC HTML report for read 1."
    info: null
    default:
    - "fastqc_raw/$id.read_1.fastqc.html"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--fastqc_html_2"
    description: "FastQC HTML report for read 2."
    info: null
    default:
    - "fastqc_raw/$id.read_2.fastqc.html"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--fastqc_zip_1"
    description: "FastQC report archive for read 1."
    info: null
    default:
    - "fastqc_raw/$id.read_1.fastqc.zip"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--fastqc_zip_2"
    description: "FastQC report archive for read 2."
    info: null
    default:
    - "fastqc_raw/$id.read_2.fastqc.zip"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--trim_html_1"
    info: null
    default:
    - "fastqc_trim/$id.read_1.trimmed_fastqc.html"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--trim_html_2"
    info: null
    default:
    - "fastqc_trim/$id.read_2.trimmed_fastqc.html"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--trim_zip_1"
    info: null
    default:
    - "fastqc_trim/$id.read_1.trimmed_fastqc.zip"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--trim_zip_2"
    info: null
    default:
    - "fastqc_trim/$id.read_2.trimmed_fastqc.zip"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--trim_log_1"
    info: null
    default:
    - "trimgalore/$id.read_1.trimming_report.txt"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--trim_log_2"
    info: null
    default:
    - "trimgalore/$id.read_2.trimming_report.txt"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--fastp_trim_json"
    description: "The fastp json format report file name"
    info: null
    default:
    - "fastp/$id_out.json"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--fastp_trim_html"
    description: "The fastp html format report file name"
    info: null
    default:
    - "fastp/$id_out.html"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--sortmerna_log"
    description: "Sortmerna log file."
    info: null
    default:
    - "sortmerna/$id.log"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--star_alignment"
    info: null
    default:
    - "STAR/$id"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--genome_bam_sorted"
    info: null
    default:
    - "STAR/genome_processed/$id.genome.bam"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--genome_bam_index"
    info: null
    default:
    - "STAR/genome_processed/$id.genome.bam.bai"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--transcriptome_bam"
    info: null
    default:
    - "STAR/transcriptome_processed/$id.transcriptome.bam"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--transcriptome_bam_index"
    info: null
    default:
    - "STAR/transcriptome_processed/$id.transcriptome.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:
    - "samtools_stats/$id.genome.stats"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--genome_bam_flagstat"
    info: null
    default:
    - "samtools_stats/$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:
    - "samtools_stats/$id.genome.idxstats"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--transcriptome_bam_stats"
    info: null
    default:
    - "samtools_stats/$id.transcriptome.stats"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--transcriptome_bam_flagstat"
    info: null
    default:
    - "samtools_stats/$id.transcriptome.flagstat"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--transcriptome_bam_idxstats"
    info: null
    default:
    - "samtools_stats/$id.transcriptome.idxstats"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--salmon_quant_results"
    info: null
    default:
    - "STAR_Salmon/$id"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--salmon_quant_results_file"
    info: null
    default:
    - "STAR_Salmon/$id/quant.sf"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--pseudo_quant_results"
    info: null
    default:
    - "Pseudo_align_quant/$id"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--rsem_counts_gene"
    description: "Expression counts on gene level"
    info: null
    default:
    - "RSEM/$id.genes.results"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--rsem_counts_transcripts"
    description: "Expression counts on transcript level"
    info: null
    default:
    - "RSEM/$id.isoforms.results"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bam_star_rsem"
    description: "BAM file generated by STAR (from RSEM)"
    info: null
    default:
    - "RSEM/$id.STAR.genome.bam"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bam_genome_rsem"
    description: "Genome BAM file (from RSEM)"
    info: null
    default:
    - "RSEM/$id.genome.bam"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bam_transcript_rsem"
    description: "Transcript BAM file (from RSEM)"
    info: null
    default:
    - "RSEM/$id.transcript.bam"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--tpm_gene"
    info: null
    default:
    - "transcript_quantification/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:
    - "transcript_quantification/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:
    - "transcript_quantification/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:
    - "transcript_quantification/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:
    - "transcript_quantification/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:
    - "transcript_quantification/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:
    - "transcript_quantification/summarizedexperiment"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--markduplicates_metrics"
    info: null
    default:
    - "picard/$id.MarkDuplicates.metrics.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--stringtie_transcript_gtf"
    info: null
    default:
    - "stringtie/$id.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:
    - "stringtie/$id.coverage.gtf"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--stringtie_abundance"
    info: null
    default:
    - "stringtie/$id.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:
    - "stringtie/$id.ballgown"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--featurecounts"
    info: null
    default:
    - "featurecounts/$id.featureCounts.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--featurecounts_summary"
    info: null
    default:
    - "featurecounts/$id.featureCounts.txt.summary"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--featurecounts_multiqc"
    info: null
    default:
    - "featurecounts/$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:
    - "featurecounts/$id.featureCounts_rrna_mqc.tsv"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bedgraph_forward"
    info: null
    default:
    - "bedgraph/$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:
    - "bedgraph/$id.reverse.bedgraph"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bigwig_forward"
    info: null
    default:
    - "bigwig/$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:
    - "bigwig/$id.reverse.bigwig"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--preseq_output"
    info: null
    default:
    - "preseq/$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:
    - "RSeQC/bamstat/$id.mapping_quality.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--strandedness_output"
    description: "Path to output report (txt) of inferred strandedness"
    info: null
    default:
    - "RSeQC/inferexperiment/$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:
    - "RSeQC/innerdistance/$id.inner_distance.stats"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--inner_dist_output_dist"
    description: "output file (txt) with inner distances of all paired reads"
    info: null
    default:
    - "RSeQC/innerdistance/txt/$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:
    - "RSeQC/innerdistance/txt/$id.inner_distance_freq.txt"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--inner_dist_output_plot"
    description: "output file (pdf) with histogram plot of of inner distances of all\
      \ paired reads"
    info: null
    default:
    - "RSeQC/innerdistance/pdf/$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:
    - "RSeQC/innerdistance/rscript/$id.inner_distance_plot.r"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--junction_annotation_output_log"
    description: "output log of junction annotation script"
    info: null
    default:
    - "RSeQC/junctionannotation/log/$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:
    - "RSeQC/junctionannotation/rscript/$id.junction_annotation_plot.r"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--junction_annotation_output_junction_bed"
    description: "junction annotation file (bed format)"
    info: null
    default:
    - "RSeQC/junctionannotation/bed/$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:
    - "RSeQC/junctionannotation/bed/$id.junction_annotation.Interact.bed"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--junction_annotation_output_junction_sheet"
    description: "junction annotation file (xls format)"
    info: null
    default:
    - "RSeQC/junctionannotation/xls/$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:
    - "RSeQC/junctionannotation/pdf/$id.splice_events.pdf"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--junction_annotation_output_splice_junctions_plot"
    description: "plot of junctions (pdf)"
    info: null
    default:
    - "RSeQC/junctionannotation/pdf/$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:
    - "RSeQC/junctionsaturation/rscript/$id.junction_saturation_plot.r"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--junction_saturation_output_plot"
    description: "plot of junction saturation (pdf"
    info: null
    default:
    - "RSeQC/junctionsaturation/pdf/$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:
    - "RSeQC/readdistribution/$id.read_distribution.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--read_duplication_output_duplication_rate_plot_r"
    description: "R script for generating duplication rate plot"
    info: null
    default:
    - "RSeQC/readduplication/rscrpt/$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:
    - "RSeQC/readduplication/pdf/$id.duplication_rate_plot.pdf"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--read_duplication_output_duplication_rate_mapping"
    description: "Summary of mapping-based read duplication"
    info: null
    default:
    - "RSeQC/readduplication/xls/$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:
    - "RSeQC/readduplication/xls/$id.duplication_rate_sequencing.xls"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--tin_output_summary"
    description: "summary statistics (txt) of calculated TIN metrics"
    info: null
    default:
    - "RSeQC/tin/txt/$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:
    - "RSeQC/tin/xls/$id.tin.xls"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--dupradar_output_dupmatrix"
    description: "path to output file (txt) of duplicate tag counts"
    info: null
    default:
    - "dupradar/gene_data/$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:
    - "dupradar/mqc_intercept/$id.dup_intercept_mqc.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--dupradar_output_duprate_exp_boxplot"
    description: "path to output file (pdf) of distribution of expression box plot"
    info: null
    default:
    - "dupradar/box_plot/$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:
    - "dupradar/scatter_plot/$id.duprate_exp_densityplot.pdf"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--dupradar_output_duprate_exp_denscurve_mqc"
    description: "path to output file (pdf) of density curve of gene duplication multiqc"
    info: null
    default:
    - "dupradar/density_curve/$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:
    - "dupradar/histogram/$id.expression_hist.pdf"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--dupradar_output_intercept_slope"
    info: null
    default:
    - "dupradar/intercept_slope/$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:
    - "qualimap/$id.qualimap_output.pdf"
    must_exist: false
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--qualimap_output_dir"
    info: null
    default:
    - "qualimap/$id"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--deseq2_output"
    info: null
    default:
    - "deseq2_qc"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--multiqc_report"
    info: null
    default:
    - "multiqc/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/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/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: "--pseudo_counts_gene"
    info: null
    default:
    - "pseudo_alignment_quantification/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:
    - "pseudo_alignment_quantification/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:
    - "pseudo_alignment_quantification/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:
    - "pseudo_alignment_quantification/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:
    - "pseudo_alignment_quantification/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_alignment_quantification/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 viash workflow for the nf-core/rnaseq pipeline.\n"
info: null
status: "enabled"
requirements:
  commands:
  - "ps"
dependencies:
- name: "workflows/prepare_genome"
  repository:
    type: "local"
- name: "cat_fastq"
  repository:
    type: "local"
- name: "workflows/pre_processing"
  repository:
    type: "local"
- name: "workflows/genome_alignment_and_quant"
  repository:
    type: "local"
- name: "workflows/pseudo_alignment_and_quant"
  repository:
    type: "local"
- name: "workflows/post_processing"
  repository:
    type: "local"
- name: "workflows/quality_control"
  repository:
    type: "local"
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: "native"
  id: "native"
build_info:
  config: "src/workflows/rnaseq/config.vsh.yaml"
  runner: "executable"
  engine: "native"
  output: "target/executable/workflows/rnaseq"
  executable: "target/executable/workflows/rnaseq/rnaseq"
  viash_version: "0.9.0"
  git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e"
  git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq"
  dependencies:
  - "target/nextflow/workflows/prepare_genome"
  - "target/nextflow/cat_fastq"
  - "target/nextflow/workflows/pre_processing"
  - "target/nextflow/workflows/genome_alignment_and_quant"
  - "target/nextflow/workflows/pseudo_alignment_and_quant"
  - "target/nextflow/workflows/post_processing"
  - "target/nextflow/workflows/quality_control"
package_config:
  version: "multiple_fixes"
  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 := 'multiple_fixes'"
  organization: "vsh"
