New Feature POC: VALIDATE_MODEL

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_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 +1,57 @@
+process VALIDATE_MODEL {
+    tag "${models_yml}"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f5/f5ef116da0b04fc6359efa48f08b9acfc040a02d7a1ec62476c77b6db0fc1499/data' :
+        'community.wave.seqera.io/library/r-jsonlite_r-optparse_r-tidyverse_r-yaml:18dc3fc2d990206d' }"
+
+    input:
+    tuple val(meta) , path(samplesheet)
+    tuple val(meta2), path(models_yml)
+
+    output:
+    tuple val(meta), path("pheno_table.csv"), emit: pheno_table
+    tuple val(meta), path("designs.json")   , emit: designs
+    tuple val(meta), path("warnings.json")  , emit: warnings, optional: true
+    path "versions.yml"                     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    validate_model.R \\
+        --yml "${models_yml}" \\
+        --samplesheet "${samplesheet}" \\
+        ${args}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${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='.'))")
+        optparse: \$(Rscript -e "cat(paste(packageVersion('optparse'), collapse='.'))")
+        yaml: \$(Rscript -e "cat(paste(packageVersion('yaml'), collapse='.'))")
+        jsonlite: \$(Rscript -e "cat(paste(packageVersion('jsonlite'), collapse='.'))")
+    END_VERSIONS
+    """
+
+    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='.'))")
+        optparse: \$(Rscript -e "cat(paste(packageVersion('optparse'), collapse='.'))")
+        yaml: \$(Rscript -e "cat(paste(packageVersion('yaml'), collapse='.'))")
+        jsonlite: \$(Rscript -e "cat(paste(packageVersion('jsonlite'), collapse='.'))")
+    END_VERSIONS
+    """
+
+}