Add bedtools/shuffle module

modules/nf-core/bedtools/shuffle/environment.yml

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::bedtools=2.31.1

modules/nf-core/bedtools/shuffle/main.nf

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+process BEDTOOLS_SHUFFLE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--h13024bc_3':
+        'biocontainers/bedtools:2.31.1--h13024bc_3' }"
+
+    input:
+    tuple val(meta) , path(intervals)
+    tuple val(meta2), path(chrom_sizes)
+    path exclude_file
+    path include_file
+
+    output:
+    tuple val(meta), path("*.bed"), emit: bed
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args        = task.ext.args ?: ''
+    def prefix      = task.ext.prefix ?: "${meta.id}"
+    def exclude_arg = exclude_file ? "-excl $exclude_file" : ''
+    def include_arg = include_file ? "-incl $include_file" : ''
+    if ("$intervals" == "${prefix}.bed") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    """
+    bedtools \\
+        shuffle \\
+        $args \\
+        -i $intervals \\
+        -g $chrom_sizes \\
+        $exclude_arg \\
+        $include_arg \\
+        > ${prefix}.bed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bedtools: \$(bedtools --version |& sed '1!d ; s/bedtools //')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if ("$intervals" == "${prefix}.bed") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    """
+    touch ${prefix}.bed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bedtools: \$(bedtools --version |& sed '1!d ; s/bedtools //')
+    END_VERSIONS
+    """
+}

modules/nf-core/bedtools/shuffle/meta.yml

@@ -0,0 +1,80 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "bedtools_shuffle"
+description: bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file
+keywords:
+  - bed
+  - shuffleBed
+  - region
+  - fai
+  - sizes
+  - genome
+  - bases
+tools:
+  - bedtools:
+      description: |
+        A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
+      documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
+      licence: ["MIT"]
+      identifier: biotools:bedtools
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing interval information
+          e.g. [ id:'test' ]
+    - intervals:
+        type: file
+        description: Input interval (BED/GFF/VCF) file
+        pattern: "*.{bed,gff,gff3,vcf}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3003"
+          - edam: "http://edamontology.org/format_2305"
+          - edam: "http://edamontology.org/format_3016"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing genome information
+          e.g. [ id:'test' ]
+    - chrom_sizes:
+        type: file
+        description: Chromosome sizes file
+        pattern: "*{.genome,.sizes,.txt,.fai}"
+  - - exclude_file:
+        type: file
+        description: BED file containing regions to exclude
+        pattern: "*.{bed}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3003"
+  - - include_file:
+        type: file
+        description: BED file containing regions to include
+        pattern: "*.{bed}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3003"
+
+output:
+  - bed:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing interval information
+            e.g. `[ id:'sample1' ]`
+      - "*.bed":
+          type: file
+          description: BED file with shuffled intervals
+          pattern: "*.{bed}"
+          ontologies:
+            - edam: "http://edamontology.org/format_3003"
+
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@itrujnara"
+maintainers:
+  - "@itrujnara"