Add starting deseq2 differential module

modules/deseq2/differential/main.nf

@@ -0,0 +1,46 @@
+params.deseq_gene_id_col = "gene_id"
+params.deseq_sample_id_col = "experiment_accession"
+params.deseq_test = "Wald"
+params.deseq_fit_type = "parametric"
+params.deseq_sf_type = 'ratio'
+params.deseq_min_replicates_for_replace = 7
+params.deseq_use_t = 'FALSE'
+params.deseq_lfc_threshold = 0
+params.deseq_alt_hypothesis = 'greaterAbs'
+params.deseq_independent_filtering = 'TRUE'
+params.deseq_p_adjust_method = 'BH'
+params.deseq_alpha = 0.1
+params.deseq_minmu = 0.5
+params.deseq_write_normalised = 'TRUE'
+params.deseq_write_variance_stabilised = 'TRUE'
+params.deseq_vs_method = 'vst'
+
+process DESEQ2_DIFFERENTIAL {
+    tag "$meta"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::bioconductor-deseq2=1.28.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bioconductor-deseq2%3A1.28.0--r40h5f743cb_0' :
+        'quay.io/biocontainers/bioconductor-deseq2:1.28.0--r40h5f743cb_0' }"
+
+    input:
+    path samplesheet
+    path counts
+    val meta
+
+    output:
+    tuple val(meta), path("deseq2.results.tsv")               , emit: results
+    tuple val(meta), path("deseq2.dispersion.png")            , emit: dispersion_plot
+    tuple val(meta), path("dds.rld.RData")                    , emit: rdata
+    tuple val(meta), path("deseq2.sizefactors.tsv")           , emit: size_factors
+    tuple val(meta), path("normalised_counts.tsv")            , emit: normalised_counts
+    tuple val(meta), path("variance_stabilised_counts.tsv")   , emit: variance_stabilised_counts
+    tuple val(meta), path("R_sessionInfo.log")                , emit: session_info
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    template 'deseq_de.r'
+}

modules/deseq2/differential/meta.yml

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+name: "deseq2_differential"
+description: runs a differential expression analysis with DESeq2
+keywords:
+  - differential
+  - expression
+  - rna-seq
+
+tools:
+  - "deseq2":
+      description: "Differential gene expression analysis based on the negative binomial distribution"
+      homepage: "https://bioconductor.org/packages/release/bioc/html/DESeq2.html"
+      documentation: "https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html"
+      tool_dev_url: "https://github.com/mikelove/DESeq2"
+      doi: "10.1186/s13059-014-0550-8"
+      licence: "['LGPL >=3']"
+
+input:
+  - sample:
+      type: file
+      description: |
+        CSV-format sample sheet with sample metadata
+  - counts:
+      type: file
+      description: |
+        Raw TSV-format expression matrix as output from the nf-core RNA-seq workflow
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing contrast information
+        e.g. [ variable:'treamtent', reference:'treated', control:'saline', blocking:'' ]
+
+output:
+  - results:
+      type: file
+      description: TSV-format table of differential expression information as output by DESeq2
+      pattern: "deseq2.results.tsv"
+  - dispersion_plot:
+      type: file
+      description: DESeq2 dispersion plot
+      pattern: "deseq2.dispersion.png"
+  - rdata:
+      type: file
+      description: Serialised DESeq2 object
+      pattern: "dds.rld.RData"
+  - sizefactors:
+      type: file
+      description: Size factors
+      pattern: "deseq2.sizefactors.tsv"
+  - normalised_counts:
+      type: file
+      description: TSV-format counts matrix, normalised to size factors
+      pattern: "normalised_counts.tsv"
+  - variance_stabilised_counts:
+      type: file
+      description: TSV-format counts matrix, normalised to size factors, with variance stabilisation applied
+      pattern: "variance_stabilised_counts.tsv"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@pinin4fjords"