feat: add chaintools-score

modules/nextflow/chaintools/score/main.nf

@@ -0,0 +1,65 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    CHAINTOOLS_SCORE — Remove chains that are primiarily the result of
+    repeats of degenerated DNA. Output is a suffixed .scored.chain file.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process CHAINTOOLS_SCORE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/alejandrogzi/chaintools:latest' }"
+
+    input:
+    tuple val(meta), path(chain)
+    tuple val(meta1), path(reference)
+    tuple val(meta2), path(query)
+
+    output:
+    tuple val(meta), path("*.scored.chain")       , optional: true, emit: chain
+    tuple val(meta), path("*.scored.chain.gz")    , optional: true, emit: chain_gz
+    path "versions.yml"                             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    chaintools score \\
+        $args \\
+        --chain $chain \\
+        --reference $reference \\
+        --query $query \\
+        --threads ${task.cpus} \\
+        --sort-by-score \\
+        --out-chain ${prefix}.scored.chain
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        chaintools: \$( chaintools --version | sed 's/chaintools //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.scored.chain
+    touch ${prefix}.scored.chain.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        chaintools: \$( chaintools --version | sed 's/chaintools //g' )
+    END_VERSIONS
+    """
+}

modules/wdl/chaintools/score/main.wdl

@@ -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.
+
+# CHAINTOOLS_SCORE — Remove chains that are primiarily the result of
+# repeats of degenerated DNA. Output is a suffixed .scored.chain file.
+
+version 1.3
+
+task score {
+  input {
+    File chain
+    File reference
+    File query
+    Int threads = 1
+    String extra_args = ""
+  }
+
+  String prefix = sub(basename(chain, ".gz"), "\\.chain$", "")
+  String out_chain = prefix + ".scored.chain"
+
+  command <<<
+    set -euo pipefail
+
+    chaintools score \
+      --chain ~{chain} \
+      --reference ~{reference} \
+      --query ~{query} \
+      --threads ~{threads} \
+      --sort-by-score \
+      --out-chain ~{out_chain} \
+      ~{extra_args}
+  >>>
+
+  output {
+    File scored_chain = out_chain
+    File scored_chain_gz = out_chain + ".gz"
+  }
+
+  requirements {
+    container: "ghcr.io/alejandrogzi/chaintools:latest"
+  }
+}
+
+workflow run {
+  input {
+    File chain
+    File reference
+    File query
+    Int threads = 1
+    String extra_args = ""
+  }
+
+  call score {
+    input:
+      chain = chain,
+      reference = reference,
+      query = query,
+      threads = threads,
+      extra_args = extra_args
+  }
+
+  output {
+    File scored_chain = score.scored_chain
+    File scored_chain_gz = score.scored_chain_gz
+  }
+}