Add module: GTFSORT (#5237)

* Initial commit

* Fix formatting

modules/nf-core/gtfsort/environment.yml

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "gtfsort"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::gtfsort=0.2.2"

modules/nf-core/gtfsort/main.nf

@@ -0,0 +1,49 @@
+process GTFSORT {
+    tag "$gtf"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gtfsort:0.2.2--h4ac6f70_0':
+        'biocontainers/gtfsort:0.2.2--h4ac6f70_0' }"
+
+    input:
+
+    path gtf
+
+    output:
+    path "*.sorted.gtf", emit: gtf
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${gtf.baseName}"
+
+    """
+    gtfsort \\
+        -i $gtf \\
+        -o ${prefix}.sorted.gtf \\
+        -t $task.cpus
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gtfsort: \$(gtfsort --version |& sed 's/gtfsort //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${gtf.baseName}"
+
+    """
+    touch ${prefix}.sorted.gtf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gtfsort: \$(gtfsort --version |& sed 's/gtfsort //')
+    END_VERSIONS
+    """
+}

modules/nf-core/gtfsort/meta.yml

@@ -0,0 +1,34 @@
+---
+name: "gtfsort"
+description: Sort GTF files in chr/pos/feature order
+keywords:
+  - sort
+  - example
+  - genomics
+tools:
+  - "gtfsort":
+      description: "A chr/pos/feature GTF sorter that uses a lexicographically-based index ordering algorithm."
+      homepage: "https://github.com/alejandrogzi/gtfsort"
+      documentation: "https://github.com/alejandrogzi/gtfsort"
+      tool_dev_url: "https://github.com/alejandrogzi/gtfsort"
+      licence: ["MIT"]
+
+input:
+  - gtf:
+      type: file
+      description: Unsorted GTF/GFF file.
+      pattern: "*.gtf"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - gtf:
+      type: file
+      description: Sorted GTF file
+      pattern: "*.gtf"
+authors:
+  - "@georgiakes"
+maintainers:
+  - "@georgiakes"

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

@@ -0,0 +1,51 @@
+nextflow_process {
+
+    name "Test Process GTFSORT"
+    script "../main.nf"
+    process "GTFSORT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gtfsort"
+
+    test("hsapiens - gtf") {
+
+        when {
+            process {
+                """
+                input[0] = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("hsapiens - gtf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/gtfsort/tests/tags.yml

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