Added tantan module

modules/nf-core/tantan/environment.yml

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "tantan"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::tantan=50"

modules/nf-core/tantan/main.nf

@@ -0,0 +1,65 @@
+process TANTAN {
+    tag "${meta.id}"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/tantan:50--h43eeafb_0':
+        'biocontainers/tantan:50--h43eeafb_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("${prefix}.fasta.gz") , optional:true , emit: masked_fasta
+    tuple val(meta), path("${prefix}.tsv")      , optional:true , emit: repeat_probs
+    tuple val(meta), path("${prefix}.tsv")      , optional:true , emit: repeat_counts
+    tuple val(meta), path("${prefix}.bed")      , optional:true , emit: bed
+    tuple val(meta), path("${prefix}.fasta.gz") , optional:true , emit: tandem_repeats
+    path "versions.yml"                                         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args            = task.ext.args ?: ''
+    def format_pattern  = /(-f)+\s+(\d)/
+    def format_matcher  = (args =~ format_pattern)
+    def format_num      = format_matcher[0][2]
+    def output_format   = format_num == 1 || format_num == 2 ? ( format_num == 3 ? "bed" : "tsv" ) : "fasta"
+    prefix              = task.ext.prefix ?: "${meta.id}"
+    """
+    tantan \\
+        ${fasta} \\
+        ${args} > ${prefix}.${output_format}
+
+    if [ -f ${prefix}.fasta ]; then
+        gzip ${prefix}.fasta
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tantan: \$(tantan --version 2>&1 | sed 's/^.*tantan //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args            = task.ext.args ?: ''
+    def format_pattern  = /(-f)+\s+(\d)/
+    def format_matcher  = (args =~ format_pattern)
+    def format_num      = format_matcher[0][2]
+    def output_format   = format_num == 1 || format_num == 2 ? ( format_num == 3 ? "bed" : "tsv" ) : "fasta"
+    prefix              = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.${output_format}
+
+    if [ -f ${prefix}.fasta ]; then
+        gzip ${prefix}.fasta
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tantan: \$(tantan --version 2>&1 | sed 's/^.*tantan //')
+    END_VERSIONS
+    """
+}

modules/nf-core/tantan/meta.yml

@@ -0,0 +1,47 @@
+name: "tantan"
+description: "Identify simple regions / low complexity / tandem repeats in DNA or protein sequences."
+keywords:
+  - mask
+  - repeat
+  - tandem
+  - complexity
+tools:
+  - "tantan":
+      description: "tantan masks simple regions (low complexity & short-period tandem repeats) in biological sequences."
+      homepage: "https://gitlab.com/mcfrith/tantan/-/blob/main/README.rst"
+      documentation: "https://gitlab.com/mcfrith/tantan/-/blob/main/README.rst"
+      tool_dev_url: "https://gitlab.com/mcfrith/tantan"
+      doi: "10.1093/nar/gkq1212"
+      licence: ['GPL v3-or-later']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - fasta:
+      type: file
+      description: FASTA file containing a nucleotide sequence.
+      pattern: "*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - masked_fasta:
+    type: file
+    description: |
+      FASTA file where all masked regions are replaced
+      with lowercase letters.
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@CarsonJM"
+maintainers:
+  - "@CarsonJM"

modules/nf-core/tantan/tests/main.nf.test

@@ -0,0 +1,100 @@
+nextflow_process {
+
+    name "Test Process TANTAN"
+    script "../main.nf"
+    process "TANTAN"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "tantan"
+
+    test("sarscov2 - fasta.gz - outfmt fasta") {
+        when {
+            params {
+                tantan_args = '-f 0'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true),
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - fasta.gz - outfmt tsv") {
+        when {
+            params {
+                tantan_args = '-f 1'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true),
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - fasta.gz - outfmt bed") {
+        when {
+            params {
+                tantan_args = '-f 3'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true),
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - fasta.gz - stub") {
+        options "-stub"
+        when {
+            params {
+                tantan_args = '-f 0'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true),
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}