add bedops/gtf2bed

modules/nf-core/bedops/gtf2bed/main.nf

@@ -0,0 +1,38 @@
+
+process BEDOPS_GTF2BED {
+    tag "$gtf"
+    label 'process_low'
+
+    conda "bioconda::bedops=2.4.41"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bedops:2.4.41--h9f5acd7_0':
+        'biocontainers/bedops:2.4.41--h9f5acd7_0' }"
+
+    input:
+    path gtf
+
+    output:
+    path '*.bed'       , emit: bed
+    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}"
+
+    """
+    cat \\
+    $gtf \\
+    | gtf2bed \\
+    $args \\
+    --attribute-key=exon_id \\
+    > ${prefix}.bed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gtf2bed: \$(bedops --version | grep version | awk ' { print \$2 } ')
+    END_VERSIONS
+    """
+}

modules/nf-core/bedops/gtf2bed/meta.yml

@@ -0,0 +1,32 @@
+name: "bedops_gtf2bed"
+description: Convert gtf format to bed format
+keywords:
+  - gtf
+  - bed
+  - conversion
+tools:
+  - gtf2bed:
+      description: The gtf2bed script converts 1-based, closed [start, end] Gene Transfer Format v2.2 (GTF2.2) to sorted, 0-based, half-open [start-1, end) extended BED-formatted data.
+      homepage: https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/gtf2bed.html
+      documentation: https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/gtf2bed.html
+      tool_dev_url: https://github.com/bedops/bedops
+      doi: 10.1093/bioinformatics/bts277
+      licence: ["GPL v2"]
+
+input:
+  - gtf:
+      type: file
+      description: A reference file in GTF format
+      pattern: "*.{gtf,gtf.gz}"
+
+output:
+  - bed:
+      type: file
+      description: A reference file in BED format
+      pattern: "*.{bed}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@davidecarlson"

tests/config/pytest_modules.yml

@@ -191,6 +191,9 @@ bcftools/stats:
 beagle5/beagle:
   - modules/nf-core/beagle5/beagle/**
   - tests/modules/nf-core/beagle5/beagle/**
+bedops/gtf2bed:
+  - modules/nf-core/bedops/gtf2bed/**
+  - tests/modules/nf-core/bedops/gtf2bed/**
 bedtools/getfasta:
   - modules/nf-core/bedtools/getfasta/**
   - tests/modules/nf-core/bedtools/getfasta/**

tests/modules/nf-core/bedops/gtf2bed/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDOPS_GTF2BED } from '../../../../../modules/nf-core/bedops/gtf2bed/main.nf'
+
+workflow test_bedops_gtf2bed {
+
+    input = [
+       //[ id:'test' ], // meta map
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genes.gtf', checkIfExists: true)]
+
+    BEDOPS_GTF2BED ( input )
+}

tests/modules/nf-core/bedops/gtf2bed/nextflow.config

@@ -0,0 +1,6 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+
+}

tests/modules/nf-core/bedops/gtf2bed/test.yml

@@ -0,0 +1,9 @@
+- name: bedops gtf2bed test_bedops_gtf2bed
+  command: nextflow run ./tests/modules/nf-core/bedops/gtf2bed -entry test_bedops_gtf2bed -c ./tests/config/nextflow.config
+  tags:
+    - bedops
+    - bedops/gtf2bed
+  files:
+    - path: output/bedops/genes.bed
+      md5sum: b783320a6ebde0b139f8e0a821b76240
+    - path: output/bedops/versions.yml