From 65b85d836d66c796f61efe0a745454a0d9da7a55 Mon Sep 17 00:00:00 2001
From: alejandrogzi <jose.gonzalesdezavala1@unmsm.edu.pe>
Date: Tue, 21 Apr 2026 17:31:27 +0200
Subject: [PATCH] feat: add cesar2

---
 modules/nextflow/cesar2/main.nf | 56 +++++++++++++++++++++++++++++++
 modules/wdl/cesar2/main.wdl     | 59 +++++++++++++++++++++++++++++++++
 2 files changed, 115 insertions(+)
 create mode 100644 modules/nextflow/cesar2/main.nf
 create mode 100644 modules/wdl/cesar2/main.wdl

diff --git a/modules/nextflow/cesar2/main.nf b/modules/nextflow/cesar2/main.nf
new file mode 100644
index 0000000..c63f9a3
--- /dev/null
+++ b/modules/nextflow/cesar2/main.nf
@@ -0,0 +1,56 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    CESAR2 — Generate chromosome size files from genome FASTA.
+    Extracts sequence lengths from a FASTA genome and outputs a chrom.sizes
+    file required by many UCSC tools.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process CESAR2 {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' : 
+        'ghcr.io/hillerlab/cesar2:latest' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*aln*"), emit: cesar2
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    cesar \\
+        $args \\
+        --max-memory ${task.memory} \\
+        $fasta
+        
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cesar: \$(cesar --version | sed -e "s/cesar v//g")
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch *aln*
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cesar: \$(cesar --version | sed -e "s/cesar v//g")
+    END_VERSIONS
+    """
+}
diff --git a/modules/wdl/cesar2/main.wdl b/modules/wdl/cesar2/main.wdl
new file mode 100644
index 0000000..94b67a8
--- /dev/null
+++ b/modules/wdl/cesar2/main.wdl
@@ -0,0 +1,59 @@
+# Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+# Distributed under the terms of the Apache License, Version 2.0.
+
+# CESAR2 — Generate chromosome size files from genome FASTA.
+# Extracts sequence lengths from a FASTA genome and outputs a chrom.sizes
+# file required by many UCSC tools.
+
+version 1.3
+
+task cesar2 {
+  input {
+    String meta_id
+    File fasta
+    String args = ""
+  }
+
+  command <<<
+    set -euo pipefail
+
+    cesar \
+      ~{args} \
+      --max-memory ~{memory} \
+      ~{fasta}
+
+    cat <<-END_VERSIONS > versions.yml
+    "CESAR2":
+        cesar: $(cesar --version | sed -e "s/cesar v//g")
+    END_VERSIONS
+  >>>
+
+  output {
+    File cesar = meta_id + ".fa"
+    File versions = "versions.yml"
+  }
+
+  requirements {
+    container: "ghcr.io/hillerlab/cesar2:latest"
+  }
+}
+
+workflow run {
+  input {
+    String meta_id
+    File fasta
+    String args = ""
+  }
+
+  call cesar2 {
+    input:
+      meta_id = meta_id,
+      fasta = fasta,
+      args = args
+  }
+
+  output {
+    File cesar = cesar2.cesar
+    File versions = cesar2.versions
+  }
+}
\ No newline at end of file