feat: add genepred lint/prune

modules/nextflow/genepred/lint/main.nf

@@ -0,0 +1,52 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    GENEPRED_LINT — Lint BED/GTF/GFF files
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process GENEPRED_LINT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/alejandrogzi/genepred:latest' }"
+
+    input:
+    tuple val(meta), path(file)
+
+    output:
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    genepred \\
+        lint \\
+        $args \\
+        $file
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        genepred: \$( genepred --version | sed 's/genepred //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        genepred: \$( genepred --version | sed 's/genepred //g' )
+    END_VERSIONS
+    """
+}

modules/nextflow/genepred/prune/main.nf

@@ -0,0 +1,57 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    GENEPRED_PRUNE — Prune BED/GTF/GFF files
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process GENEPRED_LINT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/alejandrogzi/genepred:latest' }"
+
+    input:
+    tuple val(meta), path(file)
+
+    output:
+    tuple val(meta), path("*.pruned.bed"), emit: bed
+    path "versions.yml",                   emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    genepred \\
+        lint \\
+        $args \\
+        --prune \\
+        $file > ${prefix}.pruned.bed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        genepred: \$( genepred --version | sed 's/genepred //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.pruned.bed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        genepred: \$( genepred --version | sed 's/genepred //g' )
+    END_VERSIONS
+    """
+}

modules/wdl/genepred/lint/main.wdl

@@ -0,0 +1,45 @@
+# Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+# Distributed under the terms of the Apache License, Version 2.0.
+
+# GENEPRED_LINT — Lint BED/GTF/GFF files.
+
+version 1.3
+
+task genepred_lint {
+  input {
+    File file
+    String args = ""
+  }
+
+  command <<<
+    set -euo pipefail
+
+    genepred \
+        lint \
+        ~{args} \
+        ~{file}
+  >>>
+
+  output {
+  }
+
+  requirements {
+    container: "ghcr.io/alejandrogzi/genepred:latest"
+  }
+}
+
+workflow run {
+  input {
+    File file
+    String args = ""
+  }
+
+  call genepred_lint {
+    input:
+      file = file,
+      args = args
+  }
+
+  output {
+  }
+}

modules/wdl/genepred/prune/main.wdl

@@ -0,0 +1,51 @@
+# Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+# Distributed under the terms of the Apache License, Version 2.0.
+
+# GENEPRED_PRUNE — Prune BED/GTF/GFF files.
+
+version 1.3
+
+task genepred_prune {
+  input {
+    File file
+    String args = ""
+    String prefix = basename(file, ".bed")
+  }
+
+  command <<<
+    set -euo pipefail
+
+    genepred \
+        lint \
+        ~{args} \
+        --prune \
+        ~{file} > ~{prefix}.pruned.bed
+  >>>
+
+  output {
+    File bed = prefix + ".pruned.bed"
+  }
+
+  requirements {
+    container: "ghcr.io/alejandrogzi/genepred:latest"
+  }
+}
+
+workflow run {
+  input {
+    File file
+    String args = ""
+    String prefix = basename(file, ".bed")
+  }
+
+  call genepred_prune {
+    input:
+      file = file,
+      args = args,
+      prefix = prefix
+  }
+
+  output {
+    File bed = genepred_prune.bed
+  }
+}