Isotools adapter

modules/nextflow/isotools/adapter/main.nf

@@ -0,0 +1,60 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    ISOTOOLS_ADAPTER — Detect and optionally remove adapter sequences from
+    soft-clipped regions of long-read BAM alignments.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process ISOTOOLS_ADAPTER {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/alejandrogzi/isotools:latest' }"
+
+    input:
+    tuple val(meta), path(bam)
+    tuple val(meta1), path(bai)
+
+    output:
+    tuple val(meta), path("*.without_adapters.bam"), path("*.bai"), optional: true, emit: files
+    tuple val(meta), path("*.without_adapters.bam"),                optional: true, emit: bam
+    tuple val(meta), path("*.bai"),                                 optional: true, emit: bai
+    path "versions.yml",                                            emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    iso-adapter \\
+        $args \\
+        --threads ${task.cpus} \\
+        --out-bam . \\
+        $bam 
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        iso-adapter: \$( iso-adapter --version | sed 's/iso-adapter //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch *.without_adapters.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        iso-adapter: \$( iso-adapter --version | sed 's/iso-adapter //g' )
+    END_VERSIONS
+    """
+}

modules/wdl/isotools/adapter/main.wdl

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+# Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+# Distributed under the terms of the Apache License, Version 2.0.
+
+# ISOTOOLS_ADAPTER — Detect and optionally remove adapter sequences from
+# soft-clipped regions of long-read BAM alignments.
+
+version 1.3
+
+task isotools_adapter {
+  input {
+    File bam
+    File bai
+    String args = ""
+    String prefix = sub(basename(bam), "\\.bam$", "")
+  }
+
+  command <<<
+    set -euo pipefail
+
+    iso-adapter \
+        ~{args} \
+        --threads ~{cpus} \
+        --out-bam . \
+        ~{bam}
+  >>>
+
+  output {
+    File bam_out = prefix + ".without_adapters.bam"
+    File? bai_out = prefix + ".bai"
+  }
+
+  requirements {
+    container: "ghcr.io/alejandrogzi/isotools:latest"
+  }
+}
+
+workflow run {
+  input {
+    File bam
+    File bai
+    String args = ""
+  }
+
+  call isotools_adapter {
+    input:
+      bam = bam,
+      bai = bai,
+      args = args
+  }
+
+  output {
+    File bam_out = isotools_adapter.bam_out
+    File? bai_out = isotools_adapter.bai_out
+  }
+}