Add module seqfu/stats (nf-core#5275)

* seqfu/stats

* fix test

* improve-tests

* improve-tests-fixsnap

* Update modules/nf-core/seqfu/stats/main.nf

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/seqfu/stats/main.nf

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/seqfu/stats/tests/main.nf.test

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/seqfu/stats/tests/main.nf.test

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

---------

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

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

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "seqfu_stats"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::seqfu=1.20.3"

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

@@ -0,0 +1,51 @@
+process SEQFU_STATS {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/seqfu:1.20.3--h1eb128b_0':
+        'biocontainers/seqfu:1.20.3--h1eb128b_0' }"
+
+
+    input:
+    // stats can get one or more fasta or fastq files
+    tuple val(meta), path(files)
+
+    output:
+    tuple val(meta), path("*.tsv")    ,  emit: stats
+    tuple val(meta), path("*_mqc.txt"), emit: multiqc
+    path "versions.yml"               ,  emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    seqfu \\
+        stats \\
+        $args \\
+        --multiqc ${prefix}_mqc.txt \\
+        $files > ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqfu: \$(seqfu version)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_mqc.txt
+    seqfu stats ${prefix}_mqc.txt > ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqfu: \$(samtools --version |& sed '1!d ; s/samtools //')
+    END_VERSIONS
+    """
+}

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

@@ -0,0 +1,57 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "seqfu_stats"
+description: Statistics for FASTA or FASTQ files
+keywords:
+  - seqfu
+  - stats
+  - n50
+tools:
+  - "seqfu":
+      description: "Cross-platform compiled suite of tools to manipulate and inspect FASTA and FASTQ files"
+      homepage: "https://telatin.github.io/seqfu2/"
+      documentation: "https://telatin.github.io/seqfu2/"
+      tool_dev_url: "https://github.com/telatin/seqfu2"
+      doi: "10.3390/bioengineering8050059"
+      licence: ["GPL v3"]
+
+input:
+  # Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - files:
+      type: file
+      description: One or more FASTA or FASTQ files
+      pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fq,fq.gz}"
+
+output:
+  #Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+  - stats:
+      type: file
+      description: Tab-separated output file with basic sequence statistics.
+      pattern: "*.{tsv}"
+
+  - multiqc:
+      type: file
+      description: MultiQC ready table
+      pattern: "*.{_mqc.txt}"
+
+authors:
+  - "@telatin"
+maintainers:
+  - "@telatin"

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

@@ -0,0 +1,75 @@
+nextflow_process {
+
+    name "Test Process SEQFU_STATS"
+    script "../main.nf"
+    process "SEQFU_STATS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "seqfu"
+    tag "seqfu/stats"
+
+
+    test("seqfu stats - faa") {
+        // test with 1 FAA file (with  multiple sequences of different length)
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], 
+                    file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.stats },
+                { assert process.out.multiqc },
+                { assert process.out.stats.size() == 1 },
+                { assert snapshot(process.out.versions).match("versions-single") },
+                { assert snapshot(process.out.stats).match("stats-single") },
+                { assert path(process.out.stats.get(0).get(1)).md5 == "26141ef87ad8a6f59a6f283cc0a06fda" }
+            )
+        }
+
+    }
+
+    test("seqfu stats - multiple files") {
+        // test feeding a mix of files including compressed
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test' ],
+                            [
+                                file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true),
+                                file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+                                file(params.test_data['sarscov2']['genome']['genome_fasta_gz'], checkIfExists: true),
+                                file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                            ]
+                        ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.stats },
+                { assert process.out.multiqc },
+                { assert process.out.stats.size() == 1 },
+                { assert path(process.out.versions[0]).readLines()[1].contains('.') },
+                { assert snapshot(process.out.stats).match("stats-multi") },
+                { assert snapshot(process.out.stats).md5().match("multi-lines") },
+                { assert path(process.out.stats[0][1]).readLines()[0] ==  'File\t#Seq\tTotal bp\tAvg\tN50\tN75\tN90\tauN\tMin\tMax' },
+                { assert path(process.out.multiqc[0][1]).readLines().join('\n').contains('genome.fasta') },
+                { assert path(process.out.multiqc[0][1]).readLines().join('\n').contains('proteome.fasta') }              
+            )
+        }
+
+    }
+
+}

modules/nf-core/seqfu/stats/tests/tags.yml

@@ -0,0 +1,2 @@
+seqfu/stats:
+  - "modules/nf-core/seqfu/stats/**"