From d8680b736de21f57b34ad3e693dc32e4ef601c04 Mon Sep 17 00:00:00 2001
From: John Sundh <john.sundh@scilifelab.se>
Date: Mon, 4 Mar 2024 17:30:32 +0100
Subject: [PATCH] Add mash_db option to gtdb-tk

---
 config/config.yaml         | 2 ++
 workflow/rules/binning.smk | 5 +++--
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/config/config.yaml b/config/config.yaml
index e774eeb..911c359 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -240,6 +240,8 @@ binning:
   checkm: False
   # run gtdbtk to classify bins phylogenetically?
   gtdbtk: False
+  # run with mashdb as in latest versions of GTDB-TK
+  mash: False
   # calculate average nucleotide identity for binned genomes with fastANI?
   fastani: False
 
diff --git a/workflow/rules/binning.smk b/workflow/rules/binning.smk
index ec6c6a7..6b27a49 100644
--- a/workflow/rules/binning.smk
+++ b/workflow/rules/binning.smk
@@ -514,7 +514,8 @@ rule gtdbtk_classify:
         suff='fa',
         indir=lambda wildcards, input: os.path.dirname(input.tsv),
         dbdir=lambda wildcards, input: os.path.abspath(os.path.dirname(os.path.dirname(input.met))),
-        outdir=lambda wildcards, output: os.path.dirname(output[0])
+        outdir=lambda wildcards, output: os.path.dirname(output[0]),
+        mash="--mash_db resources/gtdb/mash" if "mash" in config["binning"].keys() and config["binning"]["mash"] else "",
     threads: 20
     resources:
         runtime=lambda wildcards, attempt: attempt**2*60
@@ -530,7 +531,7 @@ rule gtdbtk_classify:
             export GTDBTK_DATA_PATH={params.dbdir}
             gtdbtk classify_wf -x {params.suff} --out_dir {params.outdir} \
                 --cpus {threads} --pplacer_cpus {threads} \
-                --genome_dir {params.indir} > {log} 2>&1
+                --genome_dir {params.indir} {params.mash} > {log} 2>&1
         fi
         """