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| 1 | +--- |
| 2 | +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json |
| 3 | +name: "deseq2_qc" |
| 4 | +description: | |
| 5 | + DESeq2-based sample QC: build a DESeq2 dataset from a gene-level count matrix and emit |
| 6 | + PCA value tables, sample-distance matrices, the corresponding diagnostic PDFs and RData |
| 7 | + objects, and the gene-level size factors. The PCA and clustering outputs are also |
| 8 | + re-emitted as MultiQC-compatible TSVs (header prepended, file/heading labels rewritten |
| 9 | + from a caller-supplied `args2` label so reports stay disambiguated per quantification |
| 10 | + source - e.g. `star_salmon` vs `salmon`). |
| 11 | +keywords: |
| 12 | + - deseq2 |
| 13 | + - qc |
| 14 | + - pca |
| 15 | + - clustering |
| 16 | + - rnaseq |
| 17 | +tools: |
| 18 | + - "r-base": |
| 19 | + description: "Base R distribution" |
| 20 | + homepage: "https://www.r-project.org/" |
| 21 | + documentation: "https://www.r-project.org/other-docs.html" |
| 22 | + licence: |
| 23 | + - "GPL v2" |
| 24 | + identifier: "" |
| 25 | + - "bioconductor-deseq2": |
| 26 | + description: "Differential gene expression analysis based on the negative binomial distribution" |
| 27 | + homepage: "https://bioconductor.org/packages/DESeq2/" |
| 28 | + documentation: "https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html" |
| 29 | + tool_dev_url: "https://github.com/thelovelab/DESeq2" |
| 30 | + doi: "10.1186/s13059-014-0550-8" |
| 31 | + licence: |
| 32 | + - "LGPL v3" |
| 33 | + identifier: "" |
| 34 | +input: |
| 35 | + - - counts: |
| 36 | + type: file |
| 37 | + description: | |
| 38 | + Gene-level raw count matrix (samples on columns, genes on rows) - typically the |
| 39 | + `*.gene_counts.tsv` output of the rnaseq tximport step. |
| 40 | + pattern: "*.{tsv,txt}" |
| 41 | + ontologies: [] |
| 42 | + - - pca_header_multiqc: |
| 43 | + type: file |
| 44 | + description: | |
| 45 | + MultiQC custom-content header file prepended to the PCA values TSV so MultiQC |
| 46 | + renders a labelled scatter plot. |
| 47 | + pattern: "*.txt" |
| 48 | + ontologies: [] |
| 49 | + - - clustering_header_multiqc: |
| 50 | + type: file |
| 51 | + description: | |
| 52 | + MultiQC custom-content header file prepended to the sample-distance matrix so |
| 53 | + MultiQC renders a labelled heatmap. |
| 54 | + pattern: "*.txt" |
| 55 | + ontologies: [] |
| 56 | +output: |
| 57 | + pdf: |
| 58 | + - "*.pdf": |
| 59 | + type: file |
| 60 | + description: Diagnostic plots (PCA biplot, sample-distance heatmap, library-size barplot) |
| 61 | + pattern: "*.pdf" |
| 62 | + ontologies: [] |
| 63 | + rdata: |
| 64 | + - "*.RData": |
| 65 | + type: file |
| 66 | + description: Serialised DESeq2 dataset (`dds`) and intermediate R objects |
| 67 | + pattern: "*.RData" |
| 68 | + ontologies: [] |
| 69 | + pca_txt: |
| 70 | + - "*pca.vals.txt": |
| 71 | + type: file |
| 72 | + description: Tab-separated PCA component values per sample |
| 73 | + pattern: "*pca.vals.txt" |
| 74 | + ontologies: [] |
| 75 | + pca_multiqc: |
| 76 | + - "*pca.vals_mqc.tsv": |
| 77 | + type: file |
| 78 | + description: PCA values TSV pre-pended with the MultiQC custom-content header |
| 79 | + pattern: "*pca.vals_mqc.tsv" |
| 80 | + ontologies: [] |
| 81 | + dists_txt: |
| 82 | + - "*sample.dists.txt": |
| 83 | + type: file |
| 84 | + description: Sample-to-sample Euclidean distance matrix |
| 85 | + pattern: "*sample.dists.txt" |
| 86 | + ontologies: [] |
| 87 | + dists_multiqc: |
| 88 | + - "*sample.dists_mqc.tsv": |
| 89 | + type: file |
| 90 | + description: Sample-distance matrix pre-pended with the MultiQC custom-content header |
| 91 | + pattern: "*sample.dists_mqc.tsv" |
| 92 | + ontologies: [] |
| 93 | + log: |
| 94 | + - "*.log": |
| 95 | + type: file |
| 96 | + description: R session info / runtime log |
| 97 | + pattern: "*.log" |
| 98 | + ontologies: [] |
| 99 | + size_factors: |
| 100 | + - "size_factors": |
| 101 | + type: directory |
| 102 | + description: Per-sample size factors written as individual `*.size_factors.RData` files |
| 103 | + pattern: "size_factors" |
| 104 | + ontologies: [] |
| 105 | + versions_r_base: |
| 106 | + - - ${task.process}: |
| 107 | + type: string |
| 108 | + description: The name of the process |
| 109 | + - r-base: |
| 110 | + type: string |
| 111 | + description: The name of the tool |
| 112 | + - "Rscript -e 'cat(as.character(getRversion()))'": |
| 113 | + type: eval |
| 114 | + description: The expression to obtain the version of the tool |
| 115 | + versions_deseq2: |
| 116 | + - - ${task.process}: |
| 117 | + type: string |
| 118 | + description: The name of the process |
| 119 | + - bioconductor-deseq2: |
| 120 | + type: string |
| 121 | + description: The name of the tool |
| 122 | + - 'Rscript -e "library(DESeq2); cat(as.character(packageVersion(''DESeq2'')))"': |
| 123 | + type: eval |
| 124 | + description: The expression to obtain the version of the tool |
| 125 | +topics: |
| 126 | + versions: |
| 127 | + - - ${task.process}: |
| 128 | + type: string |
| 129 | + description: The name of the process |
| 130 | + - r-base: |
| 131 | + type: string |
| 132 | + description: The name of the tool |
| 133 | + - "Rscript -e 'cat(as.character(getRversion()))'": |
| 134 | + type: eval |
| 135 | + description: The expression to obtain the version of the tool |
| 136 | + - - ${task.process}: |
| 137 | + type: string |
| 138 | + description: The name of the process |
| 139 | + - bioconductor-deseq2: |
| 140 | + type: string |
| 141 | + description: The name of the tool |
| 142 | + - 'Rscript -e "library(DESeq2); cat(as.character(packageVersion(''DESeq2'')))"': |
| 143 | + type: eval |
| 144 | + description: The expression to obtain the version of the tool |
| 145 | +authors: |
| 146 | + - "@drpatelh" |
| 147 | + - "@pinin4fjords" |
| 148 | +maintainers: |
| 149 | + - "@pinin4fjords" |
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