Validate YML contrasts

CHANGELOG.md

@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#345](https://github.com/nf-core/differentialabundance/pull/345)] - Plot differentially expressed genes by gene biotype ([@atrigila](https://github.com/atrigila), review by [@grst](https://github.com/grst))
 - [[#343](https://github.com/nf-core/differentialabundance/pull/343)] - Add pipeline-level nf-tests ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords) and [@nschcolnicov](https://github.com/nschcolnicov))
 - [[#286](https://github.com/nf-core/differentialabundance/pull/286)] - Integration of limma voom for rnaseq data ([@KamilMaliszArdigen](https://github.com/KamilMaliszArdigen), review by [@pinin4fjords](https://github.com/pinin4fjords))
+- [[#463](https://github.com/nf-core/differentialabundance/pull/463)] - Replace local tabulartogseachip with nf-core version. Add YML validation module. (developed by [@alanmmobbs93](https://github.com/alanmmobbs93) and [@nschcolnicov](https://github.com/nschcolnicov), review by [@grst](https://github.com/grst), [@nschcolnicov](https://github.com/nschcolnicov), [@pinin4fjords](https://github.com/pinin4fjords) and [@suzannejin](https://github.com/suzannejin))
 
 ### Fixed
 

conf/modules.config

@@ -42,6 +42,21 @@ process {
         ext.args = "--sample_id_col '${params.observations_id_col}' --feature_id_col '${params.features_id_col}'"
     }
 
+    withName: VALIDATE_YML_MODEL {
+        ext.args = {
+            params.observations_name_col ?
+            "--sample_id_col ${params.observations_name_col}" :
+            params.observations_id_col ?
+            "--sample_id_col ${params.observations_id_col}" :
+            ''
+        }
+        publishDir = [
+            path: { "${params.outdir}/validate" },
+            mode: params.publish_dir_mode,
+        ]
+
+    }
+
     withName: AFFY_JUSTRMA_RAW {
         publishDir = [
             [

modules/local/validatemodel/environment.yml

@@ -0,0 +1,8 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::r-jsonlite
+  - conda-forge::r-optparse
+  - conda-forge::r-tidyverse
+  - conda-forge::r-yaml

modules/local/validatemodel/main.nf

@@ -0,0 +1,40 @@
+process VALIDATE_YML_MODEL {
+    tag "${models_yml}"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f5/f5ef116da0b04fc6359efa48f08b9acfc040a02d7a1ec62476c77b6db0fc1499/data' :
+        'community.wave.seqera.io/library/r-jsonlite_r-optparse_r-tidyverse_r-yaml:18dc3fc2d990206d' }"
+
+    input:
+    tuple val(meta), path(samplesheet)
+    tuple val(meta2), path(models_yml)
+
+    output:
+    tuple val(meta), path("pheno_table.csv"), emit: pheno_table
+    tuple val(meta), path("designs.json")   , emit: designs
+    tuple val(meta), path("warnings.json")  , emit: warnings, optional: true
+    path "versions.yml"                     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    template 'validate_model.R'
+
+    stub:
+    """
+    touch pheno_table.csv
+    touch designs.json
+    touch warnings.json
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        r-base: \$(Rscript -e 'R.Version()\$version.string' | sed -n 's|\\[1\\] "R version \\(.*\\) (.*|\\1|p')
+        tidyverse: \$(Rscript -e "cat(paste(packageVersion('tidyverse'), collapse='.'))")
+        yaml: \$(Rscript -e "cat(paste(packageVersion('yaml'), collapse='.'))")
+        jsonlite: \$(Rscript -e "cat(paste(packageVersion('jsonlite'), collapse='.'))")
+    END_VERSIONS
+    """
+}

modules/local/validatemodel/meta.yml

@@ -0,0 +1,74 @@
+name: "validate_yml_model"
+description: "Validate a YAML model file and generate phenotype table, experimental designs, warnings, and software versions outputs."
+keywords:
+  - validation
+  - yaml
+  - model
+tools:
+  - "R":
+      description: "R programming language for statistical computing"
+      homepage: "https://www.r-project.org/"
+      licence: ["GPL >=2"]
+  - "tidyverse":
+      description: "Collection of R packages for data manipulation and visualization"
+      homepage: "https://www.tidyverse.org/"
+      licence: ["MIT"]
+  - "jsonlite":
+      description: "jsonlite: A Simple and Robust JSON Parser and Generator for R"
+      homepage: "https://cran.r-project.org/web/packages/jsonlite/index.html"
+      licence: ["MIT"]
+  - "yaml":
+      description: "yaml: Methods to Convert R Data to YAML and Back"
+      homepage: "https://cran.r-project.org/web/packages/yaml/index.html"
+      licence: ["BSD 3"]
+
+input:
+  - - meta:
+        type: map
+        description: "Groovy map containing sample metadata (e.g., [ id:'sample1' ])"
+    - samplesheet:
+        type: file
+        description: "CSV or TSV sample sheet with metadata and file names"
+        pattern: "*.csv, *.tsv"
+  - - meta2:
+        type: map
+        description: "Groovy map containing model metadata (e.g., [ id:'sample1' ])"
+    - models_yml:
+        type: file
+        description: "YAML file defining model parameters and configuration"
+        pattern: "*.yml, *.yaml"
+
+output:
+  - pheno_table:
+      - meta:
+          type: map
+          description: "Groovy map containing sample metadata"
+      - "pheno_table.csv":
+          type: file
+          description: "CSV file with phenotype table derived from the model"
+          pattern: "pheno_table.csv"
+  - designs:
+      - meta:
+          type: map
+          description: "Groovy map containing sample metadata"
+      - "designs.json":
+          type: file
+          description: "JSON file containing experimental designs"
+          pattern: "designs.json"
+  - warnings:
+      - meta:
+          type: map
+          description: "Groovy map containing sample metadata"
+      - "warnings.json":
+          type: file
+          description: "Optional JSON file with warnings and validation notes"
+          pattern: "warnings.json"
+          optional: true
+  - versions:
+      - versions.yml:
+          type: file
+          description: "YAML file recording versions of software used during validation"
+          pattern: "versions.yml"
+
+authors:
+  - "@alanmmobbs93"