From 290c1bf8b16cf2cc22e1361d52bb2c5a295938ba Mon Sep 17 00:00:00 2001
From: alejandrogzi <jose.gonzalesdezavala1@unmsm.edu.pe>
Date: Wed, 22 Apr 2026 11:34:14 +0200
Subject: [PATCH 1/2] feat: add isotools-adapter

---
 modules/nextflow/isotools/adapter/main.nf | 60 +++++++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100644 modules/nextflow/isotools/adapter/main.nf

diff --git a/modules/nextflow/isotools/adapter/main.nf b/modules/nextflow/isotools/adapter/main.nf
new file mode 100644
index 0000000..944c460
--- /dev/null
+++ b/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
+    """
+}

From 23556714c5c996c9a129922913b36a3a4bdfc598 Mon Sep 17 00:00:00 2001
From: alejandrogzi <jose.gonzalesdezavala1@unmsm.edu.pe>
Date: Wed, 22 Apr 2026 11:34:35 +0200
Subject: [PATCH 2/2] feat: add isotools-adapter

---
 modules/wdl/isotools/adapter/main.wdl | 55 +++++++++++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 modules/wdl/isotools/adapter/main.wdl

diff --git a/modules/wdl/isotools/adapter/main.wdl b/modules/wdl/isotools/adapter/main.wdl
new file mode 100644
index 0000000..5c67acf
--- /dev/null
+++ b/modules/wdl/isotools/adapter/main.wdl
@@ -0,0 +1,55 @@
+# 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
+  }
+}
\ No newline at end of file