feat: add bed2gtf

modules/nextflow/bed2gtf/main.nf

@@ -0,0 +1,67 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    BED2GTF — Convert BED to GTF.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+
+process BED2GTF {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' : 
+        'ghcr.io/alejandrogzi/bed2gtf:latest' }"
+
+    input:
+    tuple val(meta), path(bed)
+    tuple val(meta1), path(isoforms)
+
+    output:
+    tuple val(meta), path("*.gtf"),    optional: true, emit: gtf
+    tuple val(meta), path("*.gtf.gz"), optional: true, emit: gtf_gz
+    tuple val(meta), path("*.gff"),    optional: true, emit: gff
+    tuple val(meta), path("*.gff.gz"), optional: true, emit: gff_gz
+    path "versions.yml"                              , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def format = task.ext.format ?: 'gtf'
+    def prefix = task.ext.prefix ?: bed.baseName + '.' + format
+    def isf = isoforms ? "--isoforms ${isoforms}" : ''
+    """
+    bed2gtf \\
+        $args \\
+        $isf \\
+        -T ${task.cpus} \\
+        -i ${bed} \\
+        -o $prefix
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bed2gtf: \$(bed2gtf --version | sed -e "s/bed2gtf v//g")
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch *.gtf
+    touch *.gtf.gz
+    touch *.gff
+    touch *.gff.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bed2gtf: \$(bed2gtf --version | sed -e "s/bed2gtf v//g")
+    END_VERSIONS
+    """
+}

modules/nextflow/isotools/fusion/main.nf

@@ -12,7 +12,7 @@ Distributed under the terms of the Apache License, Version 2.0.
 */
 
 process ISOTOOLS_FUSION {
-    tag "$meta.id:$meta.chr"
+    tag "$meta.id"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
@@ -22,7 +22,7 @@ process ISOTOOLS_FUSION {
 
     input:
     tuple val(meta), path(bed)
-    path(reference)
+    tuple val(meta1), path(reference)
 
     output:
     tuple val(meta), path("*/fusions.bed")       , optional: true, emit: fusion
@@ -35,7 +35,7 @@ process ISOTOOLS_FUSION {
 
     script:
     def args      = task.ext.args ?: ''
-    def prefix    = task.ext.prefix ?: "${meta.id}_${meta.chr}"
+    def prefix    = task.ext.prefix ?: "${meta.id}"
     def queries   = (bed instanceof List) ? bed.join(',') : bed
     """
     iso-fusion \\

modules/nextflow/isotools/orphan/main.nf

@@ -23,52 +23,33 @@ process ISOTOOLS_ORPHAN {
     input:
     tuple val(meta), path(bed)
     tuple val(meta1), path(reference)
+    tuple val(meta2), path(splice_scores)
 
     output:
-    tuple val(meta), path("*/*.hq.bed")       , optional: true, emit: hq
-    tuple val(meta1), path("*/*.scraps.bed")  , optional: true, emit: scraps
-    path "versions.yml"                       , emit: versions
+    tuple val(meta), path("*/*.hq.bed")             , optional: true, emit: hq
+    tuple val(meta_scraps), path("*/*.scraps.bed")  , optional: true, emit: scraps
+    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 scores    = splice_scores ? "--splicing-scores $splice_scores" : ''
 
-    meta1 = meta.clone()
-    meta1.id = meta.id.split('.')[0] + '.scraps'
+    meta_scraps = meta.clone()
+    meta_scraps.id = meta.id + '.scraps'
     """
-    cut -f1-12 ${bed} > tmp.bed
-
     iso-orphan \\
         $args \\
+        $scores \\
         --ref $reference \\
         --query tmp.bed \\
         --all \\
         --threads ${task.cpus} \\
         --prefix ${prefix} 
 
-    if [ ! -s orphans/${prefix}.hq.bed ]; then
-        rm orphans/${prefix}.hq.bed
-    else
-        grep -f \\
-        <(cut -f4 orphans/${prefix}.hq.bed) ${bed} \\
-        > tmp.bed && \\
-        mv tmp.bed orphans/${prefix}.hq.bed
-    fi
-
-    if [ ! -s orphans/${prefix}.scraps.bed ]; then
-        rm orphans/${prefix}.scraps.bed
-    else
-        grep -f \\
-        <(cut -f4 orphans/${prefix}.scraps.bed) ${bed} \\
-        > tmp.bed && \\
-        mv tmp.bed orphans/${prefix}.scraps.bed
-    fi
-
-    rm tmp.bed
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         iso-orphan: \$( iso-orphan --version | sed 's/iso-orphan //g' )

modules/wdl/bed2gtf/main.wdl

@@ -0,0 +1,62 @@
+# Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+# Distributed under the terms of the Apache License, Version 2.0.
+
+# BED2GTF — Convert BED to GTF.
+# Transforms BED format files to GTF/GFF format for compatibility
+# with downstream analysis tools.
+
+version 1.3
+
+task bed2gtf {
+  input {
+    File bed
+    File? isoforms
+    String args = ""
+    String format = "gtf"
+    Int cpus = 1
+  }
+
+  String prefix = sub(basename(bed), "\\.bed$", "") + "." + format
+
+  command <<<
+    set -euo pipefail
+
+    bed2gtf \
+      ~{args} \
+      ~{"--isoforms " + isoforms} \
+      -T ~{cpus} \
+      -i ~{bed} \
+      -o ~{prefix}
+  >>>
+
+  output {
+    File gtf = prefix
+  }
+
+  requirements {
+    container: "ghcr.io/alejandrogzi/bed2gtf:latest"
+  }
+}
+
+workflow run {
+  input {
+    File bed
+    File? isoforms
+    String args = ""
+    String format = "gtf"
+    Int cpus = 1
+  }
+
+  call bed2gtf {
+    input:
+      bed = bed,
+      isoforms = isoforms,
+      args = args,
+      format = format,
+      cpus = cpus
+  }
+
+  output {
+    File gtf = bed2gtf.gtf
+  }
+}