shinyngs feature/observation matrix validation module (#2392)

* Starting component set for FOM validation module * Add test yaml * Remove trailing whitespace, bump version for bug * Cheeky symlink for testing install * [automated] Fix linting with Prettier * Revert "Cheeky symlink for testing install" This reverts commit c797d7a. * appease eclint * Fix linting issues * double quote variable in tag * Fix contrasts channel * Bump container Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Simon Pearce <[email protected]>
nf-core · Oct 31, 2022 · 72695ee · 72695ee
1 parent 6d26aab
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diff --git a/modules/nf-core/shinyngs/validatefomcomponents/main.nf b/modules/nf-core/shinyngs/validatefomcomponents/main.nf
@@ -0,0 +1,43 @@
+process SHINYNGS_VALIDATEFOMCOMPONENTS {
+    tag "$sample"
+    label 'process_single'
+
+    conda (params.enable_conda ? "bioconda::r-shinyngs=1.4.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.4.2--r41hdfd78af_0':
+        'quay.io/biocontainers/r-shinyngs:1.4.2--r41hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(sample), path(feature_meta), path(assay_files)
+    tuple val(meta2), path(contrasts)
+
+    output:
+    tuple val(meta), path("*/*.sample_metadata.tsv"), path("*/*.feature_metadata.tsv"), path("*/*.assay.tsv")   , emit: fom
+    tuple val(meta2), path("*/*.contrasts_file.tsv")                                                            , emit: contrasts
+    path "versions.yml"                                                                                         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // For full list of available args see
+    // https://github.com/pinin4fjords/shinyngs/blob/develop/exec/validate_fom_components.R
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: meta.id
+
+    """
+    validate_fom_components.R \\
+        --sample_metadata $sample \\
+        --feature_metadata $feature_meta \\
+        --assay_files ${assay_files.join(',')} \\
+        --contrasts_file $contrasts \\
+        --output_directory $prefix \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
+        r-shinyngs: \$(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/shinyngs/validatefomcomponents/meta.yml b/modules/nf-core/shinyngs/validatefomcomponents/meta.yml
@@ -0,0 +1,71 @@
+name: "shinyngs_validatefomcomponents"
+description: validate consistency of feature and sample annotations with matrices and contrasts
+
+keywords:
+  - expression
+
+tools:
+  - "shinyngs":
+      description: "Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion."
+      homepage: "https://github.com/pinin4fjords/shinyngs"
+      documentation: "https://rawgit.com/pinin4fjords/shinyngs/master/vignettes/shinyngs.html"
+      tool_dev_url: "https://github.com/pinin4fjords/shinyngs"
+      licence: "['AGPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing information on experiment, at a minimum an id.
+        e.g. [ id:'test' ]
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing information on experiment, at a minimum an id. To match meta.
+        e.g. [ id:'test' ]
+  - sample:
+      type: file
+      description: |
+        CSV-format sample sheet with sample metadata
+  - feature_meta:
+      type: file
+      description: |
+        TSV-format feature (e.g. gene) metadata
+  - assay_files:
+      type: list
+      description: |
+        List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised).
+  - contrasts:
+      type: file
+      description: |
+        CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors.
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing information on experiment.
+        e.g. [ id:'test' ]
+  - sample_meta:
+      type: file
+      description: File containing validated sample metadata
+      pattern: "/*.sample_metadata.tsv"
+  - sample_meta:
+      type: file
+      description: File containing validated feature metadata
+      pattern: "/*.feature_metadata.tsv"
+  - asays:
+      type: file
+      description: Files containing validated matrices
+      pattern: "/*.assay.tsv"
+  - contrast:
+      type: file
+      description: Files containing validated matrices
+      pattern: "/*.contrasts_file.tsv"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@pinin4fjords"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -2463,6 +2463,10 @@ shinyngs/staticexploratory:
   - modules/nf-core/shinyngs/staticexploratory/**
   - tests/modules/nf-core/shinyngs/staticexploratory/**
 
+shinyngs/validatefomcomponents:
+  - modules/nf-core/shinyngs/validatefomcomponents/**
+  - tests/modules/nf-core/shinyngs/validatefomcomponents/**
+
 shovill:
   - modules/nf-core/shovill/**
   - tests/modules/nf-core/shovill/**

diff --git a/tests/modules/nf-core/shinyngs/validatefomcomponents/main.nf b/tests/modules/nf-core/shinyngs/validatefomcomponents/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SHINYNGS_VALIDATEFOMCOMPONENTS } from '../../../../../modules/nf-core/shinyngs/validatefomcomponents/main.nf'
+
+workflow test_shinyngs_validatefomcomponents {
+
+    expression_sample_sheet = file(params.test_data['mus_musculus']['genome']['rnaseq_samplesheet'], checkIfExists: true) 
+    expression_feature_meta = file(params.test_data['mus_musculus']['genome']['rnaseq_genemeta'], checkIfExists: true) 
+    expression_matrix_file = file(params.test_data['mus_musculus']['genome']['rnaseq_matrix'], checkIfExists: true) 
+    expression_contrasts = file(params.test_data['mus_musculus']['genome']['rnaseq_contrasts'], checkIfExists: true) 
+
+    SHINYNGS_VALIDATEFOMCOMPONENTS (
+        [ [ "id":"SRP254919" ], expression_sample_sheet, expression_feature_meta,  [ expression_matrix_file ] ],
+        [ [ "id":"SRP254919" ], expression_contrasts ] 
+    )
+}
diff --git a/tests/modules/nf-core/shinyngs/validatefomcomponents/nextflow.config b/tests/modules/nf-core/shinyngs/validatefomcomponents/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/nf-core/shinyngs/validatefomcomponents/test.yml b/tests/modules/nf-core/shinyngs/validatefomcomponents/test.yml
@@ -0,0 +1,14 @@
+- name: shinyngs validatefomcomponents test_shinyngs_validatefomcomponents
+  command: nextflow run ./tests/modules/nf-core/shinyngs/validatefomcomponents -entry test_shinyngs_validatefomcomponents -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shinyngs/validatefomcomponents/nextflow.config
+  tags:
+    - shinyngs/validatefomcomponents
+    - shinyngs
+  files:
+    - path: output/shinyngs/SRP254919/SRP254919.contrasts.contrasts_file.tsv
+      md5sum: e0980240404f48216aedb63b5094029f
+    - path: output/shinyngs/SRP254919/SRP254919.gene_meta.feature_metadata.tsv
+      md5sum: 9307606b9a78af90f85b06531d190b55
+    - path: output/shinyngs/SRP254919/SRP254919.salmon.merged.gene_counts.top1000cov.assay.tsv
+      md5sum: 0c2224f6c33af1fe93c3b1382b3e05ce
+    - path: output/shinyngs/SRP254919/SRP254919.samplesheet.sample_metadata.tsv
+      md5sum: 7c5233cf34fd8eaf7071f21f6fcac7d8