From 0949a61b522b29a89d33f4be9805ccbc31ccfcae Mon Sep 17 00:00:00 2001
From: boasvdp <boasvdp@gmail.com>
Date: Fri, 23 Feb 2024 11:39:03 +0100
Subject: [PATCH] feat: allow toggling snippy --report flag

---
 bin/rules/snp_analysis.smk |  3 ++-
 juno_snp.py                | 12 ++++++++++++
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/bin/rules/snp_analysis.smk b/bin/rules/snp_analysis.smk
index 78ab30c..fb7b807 100644
--- a/bin/rules/snp_analysis.smk
+++ b/bin/rules/snp_analysis.smk
@@ -79,6 +79,7 @@ rule snp_analysis:
         basequal=13,
         maxsoft="x",
         sample="{sample}",
+        report=config["snippy"]["report"],
     shell:
         """
 snippy --cpus {threads} \
@@ -86,7 +87,7 @@ snippy --cpus {threads} \
     --ref {input.ref} \
     --R1 {input.r1} \
     --R2 {input.r2} \
-    --report \
+    {params.report} \
     --prefix {params.sample} \
     --force 2>&1>{log}
         """
diff --git a/juno_snp.py b/juno_snp.py
index ab3a724..b223e58 100644
--- a/juno_snp.py
+++ b/juno_snp.py
@@ -147,6 +147,11 @@ def _add_args_to_parser(self) -> None:
             choices=["upgma", "nj"],
             help="Algorithm to use for making the tree. It can be 'upgma' or 'nj' (neighbor-joining). Default is upgma",
         )
+        self.add_argument(
+            "--snippy-report",
+            action="store_true",
+            help="If set, the pipeline will run Snippy with --report option. This requires quite some extra time and storage, especially if there a lot of variants",
+        )
 
     def _parse_args(self) -> argparse.Namespace:
         args = super()._parse_args()
@@ -160,6 +165,7 @@ def _parse_args(self) -> argparse.Namespace:
         self.sketch_size: int = args.sketch_size
         self.mash_threshold: float = args.mash_threshold
         self.tree_algorithm: str = args.tree_algorithm
+        self.snippy_report: bool = args.snippy_report
         self.dryrun: bool = args.dryrun
 
         return args
@@ -180,6 +186,11 @@ def setup(self) -> None:
             parameters_dict = yaml.safe_load(f)
         self.snakemake_config.update(parameters_dict)
 
+        if self.snippy_report:
+            snippy_report_cmd = "--report"
+        else:
+            snippy_report_cmd = ""
+
         self.user_parameters = {
             "input_dir": str(self.input_dir),
             "output_dir": str(self.output_dir),
@@ -200,6 +211,7 @@ def setup(self) -> None:
                 "threshold": self.mash_threshold,
             },
             "tree": {"algorithm": self.tree_algorithm},
+            "snippy": {"report": snippy_report_cmd},
         }