add new module iCount-mini/metagene (nf-core#3612)

* add module template

* first version

* update testing and linting

* update file naming

* update test

* fix test

modules/nf-core/icountmini/metagene/main.nf

@@ -0,0 +1,48 @@
+process ICOUNTMINI_METAGENE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "bioconda::icount-mini=3.0.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/icount-mini:3.0.0--pyh7cba7a3_0':
+        'biocontainers/icount-mini:3.0.0--pyh7cba7a3_0' }"
+
+    input:
+    tuple val(meta), path(bed)
+    path segmentation
+
+    output:
+    tuple val(meta), path("metagene_*/*plot_data.tsv"), emit: tsv
+    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}"
+
+    """
+    mv $bed ${prefix}.bed
+
+    iCount-Mini metagene \\
+        ${prefix}.bed \\
+        $segmentation \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        iCount-Mini: \$(iCount-Mini -v)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch metagene_${prefix}/${prefix}_plot_data.tsv
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        iCount-Mini: \$(iCount-Mini -v)
+    END_VERSIONS
+    """
+}

modules/nf-core/icountmini/metagene/meta.yml

@@ -0,0 +1,44 @@
+---
+name: icountmini_metagene
+description: Plot a metagene of cross-link events/sites around various transcriptomic landmarks.
+keywords:
+  - iCLIP
+  - gtf
+  - genomics
+tools:
+  - icount:
+      description: Computational pipeline for analysis of iCLIP data
+      homepage: https://icount.readthedocs.io/en/latest/
+      documentation: https://icount.readthedocs.io/en/latest/
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bed:
+      type: file
+      description: BED file of crosslinks
+  - segmentation:
+      type: file
+      description: A iCount segmentation file
+      pattern: "*.{gtf}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - tsv:
+      type: file
+      description: Metagene table
+      pattern: "*.tsv"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@marc-jones"
+  - "@chris-cheshire"
+  - "@charlotteanne"

tests/config/pytest_modules.yml

@@ -1897,6 +1897,10 @@ ichorcna/run:
   - modules/nf-core/ichorcna/run/**
   - tests/modules/nf-core/ichorcna/run/**
 
+icountmini/metagene:
+  - modules/nf-core/icountmini/metagene/**
+  - tests/modules/nf-core/icountmini/metagene/**
+
 icountmini/peaks:
   - modules/nf-core/icountmini/peaks/**
   - tests/modules/nf-core/icountmini/peaks/**

tests/modules/nf-core/icountmini/metagene/main.nf

@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ICOUNTMINI_SEGMENT } from '../../../../../modules/nf-core/icountmini/segment/main.nf'
+include { ICOUNTMINI_METAGENE} from '../../../../../modules/nf-core/icountmini/metagene/main.nf'
+
+workflow test_icountmini_metagene {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['genome_21_gencode_gtf'], checkIfExists: true)
+    ]
+
+    ICOUNTMINI_SEGMENT ( 
+        input,
+        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+        )
+
+    bed = [
+        [  id:'test' ], // meta map
+        file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/crosslinks/clippy.bed", checkIfExists: true)
+    ]
+
+    ICOUNTMINI_METAGENE (
+        bed,
+        ICOUNTMINI_SEGMENT.out.gtf.map{ it[1] }
+    )
+}
+

tests/modules/nf-core/icountmini/metagene/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}

tests/modules/nf-core/icountmini/metagene/test.yml

@@ -0,0 +1,9 @@
+- name: icountmini metagene test_icountmini_metagene
+  command: nextflow run ./tests/modules/nf-core/icountmini/metagene -entry test_icountmini_metagene -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/icountmini/metagene/nextflow.config
+  tags:
+    - icountmini
+    - icountmini/metagene
+  files:
+    - path: output/icountmini/metagene_test/test_plot_data.tsv
+      md5sum: 63032c9e159e81f617e30bcb1c3c8509
+    - path: output/icountmini/versions.yml