rnaseq/modules/local/deseq2_qc/meta.yml at 802f166682825b2cb760afb7b447f2810e53260b · nf-core/rnaseq · GitHub

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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "deseq2_qc"
description: |
  DESeq2-based sample QC: build a DESeq2 dataset from a gene-level count matrix and emit
  PCA value tables, sample-distance matrices, the corresponding diagnostic PDFs and RData
  objects, and the gene-level size factors. The PCA and clustering outputs are also
  re-emitted as MultiQC-compatible TSVs (header prepended, file/heading labels rewritten
  from a caller-supplied `args2` label so reports stay disambiguated per quantification
  source - e.g. `star_salmon` vs `salmon`).
keywords:
  - deseq2
  - qc
  - pca
  - clustering
  - rnaseq
tools:
  - "r-base":
      description: "Base R distribution"
      homepage: "https://www.r-project.org/"
      documentation: "https://www.r-project.org/other-docs.html"
      licence:
        - "GPL v2"
      identifier: ""
  - "bioconductor-deseq2":
      description: "Differential gene expression analysis based on the negative binomial distribution"
      homepage: "https://bioconductor.org/packages/DESeq2/"
      documentation: "https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html"
      tool_dev_url: "https://github.com/thelovelab/DESeq2"
      doi: "10.1186/s13059-014-0550-8"
      licence:
        - "LGPL v3"
      identifier: ""
input:
  - - counts:
        type: file
        description: |
          Gene-level raw count matrix (samples on columns, genes on rows) - typically the
          `*.gene_counts.tsv` output of the rnaseq tximport step.
        pattern: "*.{tsv,txt}"
        ontologies: []
  - - pca_header_multiqc:
        type: file
        description: |
          MultiQC custom-content header file prepended to the PCA values TSV so MultiQC
          renders a labelled scatter plot.
        pattern: "*.txt"
        ontologies: []
  - - clustering_header_multiqc:
        type: file
        description: |
          MultiQC custom-content header file prepended to the sample-distance matrix so
          MultiQC renders a labelled heatmap.
        pattern: "*.txt"
        ontologies: []
output:
  pdf:
    - "*.pdf":
        type: file
        description: Diagnostic plots (PCA biplot, sample-distance heatmap, library-size barplot)
        pattern: "*.pdf"
        ontologies: []
  rdata:
    - "*.RData":
        type: file
        description: Serialised DESeq2 dataset (`dds`) and intermediate R objects
        pattern: "*.RData"
        ontologies: []
  pca_txt:
    - "*pca.vals.txt":
        type: file
        description: Tab-separated PCA component values per sample
        pattern: "*pca.vals.txt"
        ontologies: []
  pca_multiqc:
    - "*pca.vals_mqc.tsv":
        type: file
        description: PCA values TSV pre-pended with the MultiQC custom-content header
        pattern: "*pca.vals_mqc.tsv"
        ontologies: []
  dists_txt:
    - "*sample.dists.txt":
        type: file
        description: Sample-to-sample Euclidean distance matrix
        pattern: "*sample.dists.txt"
        ontologies: []
  dists_multiqc:
    - "*sample.dists_mqc.tsv":
        type: file
        description: Sample-distance matrix pre-pended with the MultiQC custom-content header
        pattern: "*sample.dists_mqc.tsv"
        ontologies: []
  log:
    - "*.log":
        type: file
        description: R session info / runtime log
        pattern: "*.log"
        ontologies: []
  size_factors:
    - "size_factors":
        type: directory
        description: Per-sample size factors written as individual `*.size_factors.RData` files
        pattern: "size_factors"
        ontologies: []
  versions_r_base:
    - - ${task.process}:
          type: string
          description: The name of the process
      - r-base:
          type: string
          description: The name of the tool
      - "Rscript -e 'cat(as.character(getRversion()))'":
          type: eval
          description: The expression to obtain the version of the tool
  versions_deseq2:
    - - ${task.process}:
          type: string
          description: The name of the process
      - bioconductor-deseq2:
          type: string
          description: The name of the tool
      - 'Rscript -e "library(DESeq2); cat(as.character(packageVersion(''DESeq2'')))"':
          type: eval
          description: The expression to obtain the version of the tool
topics:
  versions:
    - - ${task.process}:
          type: string
          description: The name of the process
      - r-base:
          type: string
          description: The name of the tool
      - "Rscript -e 'cat(as.character(getRversion()))'":
          type: eval
          description: The expression to obtain the version of the tool
    - - ${task.process}:
          type: string
          description: The name of the process
      - bioconductor-deseq2:
          type: string
          description: The name of the tool
      - 'Rscript -e "library(DESeq2); cat(as.character(packageVersion(''DESeq2'')))"':
          type: eval
          description: The expression to obtain the version of the tool
authors:
  - "@drpatelh"
  - "@pinin4fjords"
maintainers:
  - "@pinin4fjords"