feat: isotools-align

modules/nextflow/isotools/align/main.nf

@@ -0,0 +1,66 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    ISOTOOLS_ALIGN — Select long reads whose pass-1 split alignment suggests a
+    re-align with a larger minimap2 intron cap, and emit them as FASTA / FASTQ / names.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process ISOTOOLS_ALIGN {
+    tag "$meta.id"
+    label 'custom_process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/alejandrogzi/isotools:latest' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+
+    output:
+    tuple val(meta), path("*.fragments.fasta"),   optional: true, emit: fasta
+    tuple val(meta), path("*.report.tsv"),        optional: true, emit: report
+    path "versions.yml",                          emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    iso-align \\
+        $args \\
+        --threads ${task.cpus} \\
+        --bam $bam \\
+        --output ${prefix}.fragments.fasta \\
+        --output-format fasta \\
+        --report ${prefix}.report.tsv
+
+    if [ ! -s ${prefix}.fragments.fasta ]; then
+        rm ${prefix}.fragments.fasta 
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        iso-align: \$( iso-align --version | sed 's/iso-align //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.fragments.fasta
+    touch ${prefix}.report.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        iso-align: \$( iso-align --version | sed 's/iso-align //g' )
+    END_VERSIONS
+    """
+}

modules/wdl/isotools/align/main.wdl

@@ -0,0 +1,61 @@
+# Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+# Distributed under the terms of the Apache License, Version 2.0.
+
+# ISOTOOLS_ALIGN — Select long reads whose pass-1 split alignment suggests a
+# re-align with a larger minimap2 intron cap, and emit them as FASTA / FASTQ / names.
+
+version 1.3
+
+task align {
+  input {
+    File bam
+    File bai
+    String args = ""
+    String prefix = sub(basename(bam), "\\.bam$", "")
+  }
+
+  command <<<
+    set -euo pipefail
+
+    iso-align \
+        ~{args} \
+        --threads ~{cpus} \
+        --bam ~{bam} \
+        --output ~{prefix}.fragments.fasta \
+        --output-format fasta \
+        --report ~{prefix}.report.tsv
+
+    if [ ! -s ~{prefix}.fragments.fasta ]; then
+        rm ~{prefix}.fragments.fasta
+    fi
+  >>>
+
+  output {
+    File? fragments = prefix + ".fragments.fasta"
+    File? report = prefix + ".report.tsv"
+  }
+
+  requirements {
+    container: "ghcr.io/alejandrogzi/isotools:latest"
+  }
+}
+
+workflow run {
+  input {
+    File bam
+    File bai
+    String args = ""
+  }
+
+  call align {
+    input:
+      bam = bam,
+      bai = bai,
+      args = args
+  }
+
+  output {
+    File? fragments = align.fragments
+    File? report = align.report
+  }
+}