From 5f83ffa9629584eec33a34df87b1fb2aa2bf7b53 Mon Sep 17 00:00:00 2001
From: Ivan Blagoev Topolsky <ivan.topolsky@bsse.ethz.ch>
Date: Wed, 4 Dec 2024 15:13:21 +0100
Subject: [PATCH] [feature] lofreq parallel threads

Co-authored-by: AugusteRi <AugusteRi@gmail.com>
---
 workflow/rules/snv.smk              | 10 ++++++++--
 workflow/schemas/config_schema.json |  4 ++++
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/workflow/rules/snv.smk b/workflow/rules/snv.smk
index 2c94be8f..c7701883 100644
--- a/workflow/rules/snv.smk
+++ b/workflow/rules/snv.smk
@@ -263,6 +263,11 @@ rule lofreq:
         EXTRA=config.lofreq["extra"],
         SAMTOOLS=config.applications["samtools"],
         LOFREQ=config.applications["lofreq"],
+        kind=lambda wildcards, threads: "parallel" if threads > 1 else "old-school",
+        subcmd=lambda wildcards, threads: "call-parallel" if threads > 1 else "call",
+        threadspar=lambda wildcards, threads: (
+            f"--pp-threads {threads}" if threads > 1 else ""
+        ),
     log:
         outfile="{dataset}/variants/SNVs/lofreq.out.log",
         errfile="{dataset}/variants/SNVs/lofreq.err.log",
@@ -274,6 +279,7 @@ rule lofreq:
         disk_mb=2000,
         mem_mb=config.lofreq["mem"],
         runtime=config.lofreq["time"],
+    threads: config.lofreq["threads"]
     shell:
         """
         # Add qualities to indels
@@ -282,8 +288,8 @@ rule lofreq:
         {params.SAMTOOLS} index {output.BAM} 2> >(tee {log.errfile} >&2)
 
         # Run Lofreq
-        echo "Running LoFreq" >> {log.outfile}
-        {params.LOFREQ} call {params.EXTRA} --call-indels -f {input.REF} -o {output.SNVs} --verbose {output.BAM} >> {log.outfile} 2> >(tee -a {log.errfile} >&2)
+        echo "Running {params.kind} LoFreq ({params.subcmd})" >> {log.outfile}
+        {params.LOFREQ} "{params.subcmd}" {params.EXTRA} --call-indels {params.threadspar} -f {input.REF} -o {output.SNVs} --verbose {output.BAM} >> {log.outfile} 2> >(tee -a {log.errfile} >&2)
         """
 
 
diff --git a/workflow/schemas/config_schema.json b/workflow/schemas/config_schema.json
index b3482193..2fed877c 100644
--- a/workflow/schemas/config_schema.json
+++ b/workflow/schemas/config_schema.json
@@ -1274,6 +1274,10 @@
                     "type": "integer",
                     "default": 2000
                 },
+                "threads": {
+                    "type": "integer",
+                    "default": 4
+                },
                 "time": {
                     "type": "integer",
                     "default": 60