Add module seqfu/check

modules/nf-core/seqfu/check/environment.yml

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::seqfu=1.22.3

modules/nf-core/seqfu/check/main.nf

@@ -0,0 +1,48 @@
+process SEQFU_CHECK {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/seqfu:1.22.3--hc29b5fc_1':
+        'biocontainers/seqfu:1.22.3--hc29b5fc_1' }"
+
+    input:
+    tuple val(meta), path(fastq)
+
+    output:
+    tuple val(meta), path("*.tsv")    , emit: check
+    path "versions.yml"               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    seqfu \\
+        check \\
+        $args \\
+        $fastq > ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqfu: \$(seqfu version)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo $args
+
+    touch ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqfu: \$(seqfu version)
+    END_VERSIONS
+    """
+}

modules/nf-core/seqfu/check/meta.yml

@@ -0,0 +1,52 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "seqfu_check"
+description: "Evaluates the integrity of DNA FASTQ files."
+keywords:
+- check
+- fastq
+- fasta
+- qc
+- format
+tools:
+  - "seqfu":
+      description: "DNA sequence utilities for FASTX files"
+      homepage: "https://telatin.github.io/seqfu2/"
+      documentation: "https://telatin.github.io/seqfu2/"
+      tool_dev_url: "https://telatin.github.io/seqfu2/tools/check.html"
+      doi: "10.3390/bioengineering8050059"
+      licence: ["GPL v3"]
+      identifier: biotools:seqfu
+
+input:
+- - meta:
+      type: map
+      description: Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
+  - fastas:
+      type: file
+      description: Input files (mainly FASTA, FASTQ supported)
+      pattern: "*.{fq,fastq}[.gz]"
+      ontologies:
+      - edam: http://edamontology.org/format_2545  # FASTQ-like
+output:
+  dna_sequence:
+  - - meta:
+        type: map
+        description: Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
+    - '*.{tsv}':
+        type: file      
+        description: Output table (TSV format)
+        pattern: '*.{tsv}'
+        ontologies:
+        - edam: http://edamontology.org/format_3475  # TSV
+
+  versions:
+  - versions.yml:
+      type: file
+      description: File containing software versions
+      pattern: versions.yml
+      ontologies:
+      - edam: http://edamontology.org/format_3750  # YAML
+authors:
+- "@georgette-femerling"
+maintainers:
+- "@georgette-femerling"

modules/nf-core/seqfu/check/tests/main.nf.test

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+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core modules test seqfu/check
+nextflow_process {
+
+    name "Test Process SEQFU_CHECK"
+    script "../main.nf"
+    process "SEQFU_CHECK"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "seqfu"
+    tag "seqfu/check"
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
+    test("sarscov2 - bam") {
+
+        // TODO nf-core: If you are created a test for a chained module
+        // (the module requires running more than one process to generate the required output)
+        // add the 'setup' method here.
+        // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules).
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+                // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
+            )
+        }
+
+    }
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+            )
+        }
+
+    }
+
+}