feat(chaintools): add coverage module (nextflow + wdl)

modules/nextflow/chaintools/coverage/main.nf

@@ -0,0 +1,67 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    CHAINTOOLS_COVERAGE — Measure annotation feature coverage by aligned chain blocks.
+    Measures how many bases of annotation features (cds/exon/intron/utr) from
+    BED/GTF/GFF are covered by chain alignment blocks on the selected side
+    (reference/query) in forward genomic coordinates. Reports per-chrom and
+    total coverage fractions.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process CHAINTOOLS_COVERAGE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/alejandrogzi/chaintools:latest' }"
+
+    input:
+    tuple val(meta), path(chains)
+    path intervals
+    val side
+    val feature
+
+    output:
+    tuple val(meta), path("*.coverage.txt")    , emit: report
+    path "versions.yml"                        , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    chaintools coverage \\
+        $args \\
+        --chains $chains \\
+        --side $side \\
+        --intervals $intervals \\
+        --feature $feature \\
+        --threads ${task.cpus} \\
+        > ${prefix}.coverage.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        chaintools: \$( chaintools --version | sed 's/chaintools //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.coverage.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        chaintools: \$( chaintools --version | sed 's/chaintools //g' )
+    END_VERSIONS
+    """
+}

modules/wdl/chaintools/coverage/main.wdl

@@ -0,0 +1,73 @@
+# Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+# Distributed under the terms of the Apache License, Version 2.0.
+
+# CHAINTOOLS_COVERAGE — Measure annotation feature coverage by aligned chain blocks.
+# Measures how many bases of annotation features (cds/exon/intron/utr) from
+# BED/GTF/GFF are covered by chain alignment blocks on the selected side
+# (reference/query) in forward genomic coordinates. Reports per-chrom and
+# total coverage fractions.
+
+version 1.3
+
+task coverage {
+  input {
+    Array[File] chains
+    File intervals
+    String side
+    String feature
+    Int threads = 1
+    String extra_args = ""
+    String prefix = ""
+  }
+
+  String out_prefix = if prefix == "" then "coverage" else prefix
+  String out_report = out_prefix + ".coverage.txt"
+
+  command <<<
+    set -euo pipefail
+
+    chaintools coverage \
+      --chains ~{sep=" " chains} \
+      --side ~{side} \
+      --intervals ~{intervals} \
+      --feature ~{feature} \
+      --threads ~{threads} \
+      ~{extra_args} \
+      > ~{out_report}
+  >>>
+
+  output {
+    File report = out_report
+  }
+
+  requirements {
+    container: "ghcr.io/alejandrogzi/chaintools:latest"
+  }
+}
+
+workflow run {
+  input {
+    Array[File] chains
+    File intervals
+    String side
+    String feature
+    Int threads = 1
+    String extra_args = ""
+    String prefix = ""
+  }
+
+  call coverage {
+    input:
+      chains = chains,
+      intervals = intervals,
+      side = side,
+      feature = feature,
+      threads = threads,
+      extra_args = extra_args,
+      prefix = prefix
+  }
+
+  output {
+    File report = coverage.report
+  }
+}