feat(tiberius): add prediction, merge, and scatter workflow

assets/catalog/catalog.md

@@ -116,6 +116,10 @@
 - [annevo/decoding](../../modules/nextflow/annevo/decoding/main.nf) — Decode ANNEVO H5 predictions into GFF3 on CPU.
 - [subworkflows/annevo](../../subworkflows/annevo/main.nf) — Scatter (none / chromosome / weighted), predict, decode, and gather GFF3.
 - [workflows/annevo](../../workflows/annevo/main.nf) — Standalone ANNEVO pipeline. Bundled ANNEVO is non-commercial.
+- [tiberius/predict](../../modules/nextflow/tiberius/predict/main.nf) — Tiberius ab initio inference (`process_gpu`; CPU if no GPU profile). Scatter jobs emit GTF only.
+- [tiberius/merge](../../modules/nextflow/tiberius/merge/main.nf) — Merge chunk GTFs with merge_annotations.py, restore FASTA order, emit GTF/GFF3 and optional protein/CDS FASTAs.
+- [subworkflows/tiberius](../../subworkflows/tiberius/main.nf) — Scatter (none / chromosome / weighted), predict, and merge.
+- [workflows/tiberius](../../workflows/tiberius/main.nf) — Standalone Tiberius pipeline.
 
 ---
 

modules/nextflow/tiberius/merge/main.nf

@@ -0,0 +1,74 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    TIBERIUS_MERGE — Merge scattered Tiberius chunk annotations.
+
+    Runs merge_annotations.py (full mode), restores FASTA record order from
+    the sequence-order manifest, writes GTF, and optionally extracts
+    protein/CDS FASTAs from the merged annotation plus the original genome.
+    Gene IDs are assigned by (seqid, start, strand), not chunk order.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process TIBERIUS_MERGE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/hillerlab/tiberius:latest' }"
+
+    input:
+    tuple val(meta), path(annotations), path(manifest), path(genome)
+    val emit_protseq
+    val emit_codingseq
+
+    output:
+    tuple val(meta), path("*.gtf"),  emit: gtf
+    tuple val(meta), path("*.gff3"), emit: gff
+    tuple val(meta), path("*.prot"), emit: proteins,  optional: true
+    tuple val(meta), path("*.cds"),  emit: codingseq, optional: true
+    path "versions.yml",             emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix     = task.ext.prefix ?: "${meta.id}"
+    def prot_flag  = emit_protseq ? '--protseq' : ''
+    def cds_flag   = emit_codingseq ? '--codingseq' : ''
+    """
+    tiberius-merge \\
+        --manifest ${manifest} \\
+        --out-prefix ${prefix} \\
+        --genome ${genome} \\
+        ${prot_flag} \\
+        ${cds_flag} \\
+        ${annotations}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tiberius: \$( python3 -c "import tiberius; print(tiberius.__version__)" )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    def emit_prot = emit_protseq ? true : false
+    def emit_cds  = emit_codingseq ? true : false
+    """
+    touch ${prefix}.gtf
+    touch ${prefix}.gff3
+    ${emit_prot ? "touch ${prefix}.prot" : ''}
+    ${emit_cds ? "touch ${prefix}.cds" : ''}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tiberius: \$( python3 -c "import tiberius; print(tiberius.__version__)" 2>/dev/null || echo "2.0.7" )
+    END_VERSIONS
+    """
+}

modules/nextflow/tiberius/predict/main.nf

@@ -0,0 +1,95 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    TIBERIUS_PREDICT — Ab initio Tiberius inference.
+
+    Thin wrapper around `tiberius.py`. GPU is used when `-profile gpu`
+    exposes a device; otherwise TensorFlow falls back to CPU. Scatter jobs
+    should emit GTF only; GFF3 and protein/CDS FASTAs of a scattered run
+    come from TIBERIUS_MERGE.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process TIBERIUS_PREDICT {
+    tag "$meta.id"
+    label 'process_high'
+    label 'process_gpu'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/hillerlab/tiberius:latest' }"
+
+    input:
+    tuple val(meta), path(genome)
+    val model_cfg
+
+    output:
+    tuple val(meta), path("*.gtf"),  emit: gtf
+    tuple val(meta), path("*.gff3"), emit: gff,       optional: true
+    tuple val(meta), path("*.prot"), emit: proteins,  optional: true
+    tuple val(meta), path("*.cds"),  emit: codingseq, optional: true
+    path "versions.yml",             emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args       = [task.ext.args ?: '', meta.tiberius_args ?: ''].findAll { it }.join(' ')
+    def prefix     = task.ext.prefix ?: "${meta.id}"
+    def custom     = task.ext.model ?: (meta.model ?: '')
+    def emit_gff3  = meta.tiberius_emit_gff3 == true
+    def emit_prot  = meta.tiberius_protseq == true
+    def emit_cds   = meta.tiberius_codingseq == true
+    def out_files  = emit_gff3 ? "${prefix}.gtf ${prefix}.gff3" : "${prefix}.gtf"
+    def prot_flag  = emit_prot ? "--protseq ${prefix}.prot" : ''
+    def cds_flag   = emit_cds ? "--codingseq ${prefix}.cds" : ''
+    """
+    set -euo pipefail
+    model_args=""
+    if [ -n "${custom}" ]; then
+        model_args="--model ${custom}"
+    else
+        yaml=\$(awk -F '\\t' -v a="${model_cfg}" '\$1==a {print \$2; exit}' /opt/tiberius/models.tsv)
+        if [ -z "\$yaml" ]; then
+            echo "Unknown --model_cfg alias '${model_cfg}'. Use a hiller_alias from /opt/tiberius/models.tsv." >&2
+            awk -F '\\t' '\$1 !~ /^#/ && \$1 != "hiller_alias" {print \$1}' /opt/tiberius/models.tsv >&2
+            exit 1
+        fi
+        model_args="--model_cfg /opt/tiberius/model_cfg/\$yaml"
+    fi
+
+    tiberius.py \\
+        --genome ${genome} \\
+        \${model_args} \\
+        --out ${out_files} \\
+        ${prot_flag} \\
+        ${cds_flag} \\
+        ${args}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tiberius: \$( python3 -c "import tiberius; print(tiberius.__version__)" )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    def emit_gff3 = meta.tiberius_emit_gff3 == true
+    def emit_prot = meta.tiberius_protseq == true
+    def emit_cds  = meta.tiberius_codingseq == true
+    """
+    touch ${prefix}.gtf
+    ${emit_gff3 ? "touch ${prefix}.gff3" : ''}
+    ${emit_prot ? "touch ${prefix}.prot" : ''}
+    ${emit_cds ? "touch ${prefix}.cds" : ''}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tiberius: \$( python3 -c "import tiberius; print(tiberius.__version__)" 2>/dev/null || echo "2.0.7" )
+    END_VERSIONS
+    """
+}