added new module lofraq/viterbi; solves new module: lofreq/viterbi nf…

…-core#5158 (nf-core#5197)

* added new module lofraq/viterbi; solves new module: lofreq/viterbi nf-core#5158

* added new module lofraq/viterbi; solves new module: lofreq/viterbi nf-core#5158

* removed yml schema comments

* added samtools as conda dependency; chnaged container build version to py310h47ef89e_10; updated test snapshot

modules/nf-core/lofreq/viterbi/environment.yml

@@ -0,0 +1,8 @@
+name: "lofreq_viterbi"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::lofreq=2.1.5
+  - bioconda::samtools=1.17

modules/nf-core/lofreq/viterbi/main.nf

@@ -0,0 +1,54 @@
+process LOFREQ_VITERBI {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py310h47ef89e_10' :
+        'biocontainers/lofreq:2.1.5--py310h47ef89e_10' }"
+
+    input:
+    tuple val(meta), path(bam)
+    path(fasta)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    lofreq \\
+        viterbi \\
+        $args \\
+        -ref $fasta \\
+        $bam |
+        samtools sort \\
+            $args2 \\
+            -T ${prefix} \\
+            --threads $task.cpus \\
+            -o ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        lofreq: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        lofreq: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
+    END_VERSIONS
+    """
+}

modules/nf-core/lofreq/viterbi/meta.yml

@@ -0,0 +1,50 @@
+name: "lofreq_viterbi"
+description: Lofreq subcommand to call low frequency variants from alignments when tumor-normal paired samples are available
+keywords:
+  - variant calling
+  - low frequency variant calling
+  - variants
+  - bam
+  - probabilistic realignment
+tools:
+  - "lofreq":
+      description: "A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data"
+      homepage: https://csb5.github.io/lofreq/
+      documentation: https://csb5.github.io/lofreq/commands/
+      doi: 10.1093/nar/gks918
+      licence: ["MIT"]
+input:
+  # Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - bam:
+      type: file
+      description: Sorted BAM file
+      pattern: "*.{bam}"
+  - fasta:
+      type: file
+      description: Reference genome FASTA file
+      pattern: "*.{fasta}"
+output:
+  - 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"
+  - bam:
+      type: file
+      description: Realignment and sorted BAM file
+      pattern: "*.{bam}"
+
+authors:
+  - "@MarieLataretu"
+maintainers:
+  - "@MarieLataretu"

modules/nf-core/lofreq/viterbi/tests/main.nf.test

@@ -0,0 +1,64 @@
+nextflow_process {
+
+    name "Test Process LOFREQ_VITERBI"
+    script "../main.nf"
+    process "LOFREQ_VITERBI"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "lofreq"
+    tag "lofreq/viterbi"
+
+    test("sarscov2 - bam, fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+                    ]
+                input[1] = [
+                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam, fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+                    ]
+                input[1] = [
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/lofreq/viterbi/tests/tags.yml

@@ -0,0 +1,2 @@
+lofreq/viterbi:
+  - "modules/nf-core/lofreq/viterbi/**"