add agat/spaddintrons (#4650)

* add agat/spaddintrons

* fix linting error with prettier

* fix modules linting error in meta.yml

* Update modules/nf-core/agat/spaddintrons/meta.yml

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

* Update modules/nf-core/agat/spaddintrons/main.nf

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

* Update modules/nf-core/agat/spaddintrons/environment.yml

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

* Update modules/nf-core/agat/spaddintrons/environment.yml

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

* Update modules/nf-core/agat/spaddintrons/meta.yml

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

* Update modules/nf-core/agat/spaddintrons/meta.yml

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

* add meta map

* add meta to output and update snapshot

* add logic to use meta.id in determining output file name

* Update modules/nf-core/agat/spaddintrons/tests/main.nf.test

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

* fix logic for output file name in stub

* remove trailing whitespace

* fix snapshot

---------

Co-authored-by: Anne Marie Noronha <anoronh4@users.noreply.github.com>
Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Sateesh <perisateesh@gmail.com>

modules/nf-core/agat/spaddintrons/environment.yml

@@ -0,0 +1,7 @@
+name: agat_spaddintrons
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::agat=1.2.0"

modules/nf-core/agat/spaddintrons/main.nf

@@ -0,0 +1,51 @@
+process AGAT_SPADDINTRONS {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/agat:1.2.0--pl5321hdfd78af_0':
+        'biocontainers/agat:1.2.0--pl5321hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(gff)
+    path config
+
+    output:
+    tuple val(meta), path("${output}"), emit: gff
+    path "versions.yml"               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def config_param = config ? "--config $config" : ""
+    def prefix = meta.id ?: gff.getBaseName()
+    output = "${prefix}.intron.gff"
+    """
+    agat_sp_add_introns.pl \\
+        --gff $gff \\
+        $config_param \\
+        --out $output \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        agat: \$(agat_sp_add_introns.pl --help | sed '3!d; s/.*v//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = meta.id ?: gff.getBaseName()
+    output = "${prefix}.intron.gff"
+    """
+    touch ${output}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        agat: \$(agat_sp_add_introns.pl --help | sed '3!d; s/.*v//')
+    END_VERSIONS
+    """
+}

modules/nf-core/agat/spaddintrons/meta.yml

@@ -0,0 +1,43 @@
+name: agat_spaddintrons
+description: Add intron features to gtf/gff file without intron features.
+keywords:
+  - gtf
+  - gff
+  - introns
+tools:
+  - agat:
+      description: "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format."
+      homepage: "https://agat.readthedocs.io/en/latest/"
+      documentation: "https://agat.readthedocs.io/en/latest/"
+      tool_dev_url: "https://github.com/NBISweden/AGAT"
+      licence: ["GPL v3"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - gff:
+      type: file
+      description: Input gtf/gff file
+      pattern: "*.{gff,gff3,gtf}"
+  - config:
+      type: file
+      description: Optional input agat config file
+      pattern: "*.{yaml,yml}"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - gff:
+      type: file
+      description: Output gff3 file with introns
+      pattern: "*.gff"
+
+authors:
+  - "@anoronh4"
+maintainers:
+  - "@anoronh4"

modules/nf-core/agat/spaddintrons/tests/main.nf.test

@@ -0,0 +1,61 @@
+nextflow_process {
+
+    name "Test Process AGAT_SPADDINTRONS"
+    script "../main.nf"
+    process "AGAT_SPADDINTRONS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "agat"
+    tag "agat/spaddintrons"
+
+    test("homo_sapiens - gtf") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+                ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - gtf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+                ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.gff.collect { file(it[1]).getName() } +
+                                process.out.versions ).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/agat/spaddintrons/tests/tags.yml

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