Merge pull request SciLifeLab#431 from kedhammar/master

update anglerfish command used
aanil · Sep 2, 2024 · c08d3f3 · c08d3f3
2 parents 49d11af + 12d13ed
commit c08d3f3
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diff --git a/VERSIONLOG.md b/VERSIONLOG.md
@@ -1,5 +1,9 @@
 # TACA Version Log
 
+## 20240816.1
+
+Update command used to run Anglerfish.
+
 ## 20240705.1
 
 Add section header in samplesheet for run folder transfer

diff --git a/taca/nanopore/ONT_run_classes.py b/taca/nanopore/ONT_run_classes.py
@@ -530,10 +530,12 @@ def run_anglerfish(self):
 
         anglerfish_command = [
             self.anglerfish_path,
+            "run",
             f"--samplesheet {self.anglerfish_samplesheet}",
             f"--out_fastq {self.run_abspath}",
             f"--run_name {anglerfish_run_name}",
             f"--threads {n_threads}",
+            "--max_distance 1",
             "--lenient",
             "--skip_demux",
         ]