fix: fix trimadap-mt & bbduk java version (#446)

bihealth · Sep 20, 2023 · 46b2303 · 46b2303
1 parent 0ca23f6
commit 46b2303
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diff --git a/snappy_wrappers/wrappers/bbduk/environment.yaml b/snappy_wrappers/wrappers/bbduk/environment.yaml
@@ -3,3 +3,4 @@ channels:
   - bioconda
 dependencies:
   - bbmap =39
+  - openjdk >= 8 
diff --git a/snappy_wrappers/wrappers/bwa/wrapper.py b/snappy_wrappers/wrappers/bwa/wrapper.py
@@ -74,7 +74,7 @@
     set -x
 
     if [[ "{snakemake.config[step_config][ngs_mapping][bwa][trim_adapters]}" == "True" ]]; then
-        trimadapt-mt -p {snakemake.config[step_config][ngs_mapping][bwa][num_threads_trimming]}
+        trimadap-mt -p {snakemake.config[step_config][ngs_mapping][bwa][num_threads_trimming]}
     else
         cat  # TODO: can we somehow remove this?
     fi