perf: update to varlociraptor 8.4 (#596)

* Update to latest varlociraptor * Update varlociraptor.yaml * Update config.yaml * trigger rerun --------- Co-authored-by: Alexander Thomas <[email protected]>
IKIM-Essen · Nov 13, 2023 · 34701af · 34701af
1 parent 7106afa
commit 34701af
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diff --git a/config/config.yaml b/config/config.yaml
@@ -72,12 +72,12 @@ assembly:
     # assemblers used for shotgun sequencing with on Illumina technology
     shotgun: "megahit-std"
     # assemblers used for amplicon sequencing with on Illumina technology
-    amplicon: "metaspades"
+    amplicon: "megahit-std"
   oxford nanopore:
     # assemblers used for shotgun sequencing with on Oxford Nanopore technology
     shotgun: "megahit-std"
     # assemblers used for amplicon sequencing with on Oxford Nanopore technology
-    amplicon: "spades"
+    amplicon: "megahit-std"
     # Medaka models are named to indicate i) the pore type, ii) the sequencing device (MinION or PromethION), iii) the basecaller variant, and iv) the basecaller version
     # with the format: {pore}_{device}_{caller variant}_{caller version}
     # See https://github.com/nanoporetech/medaka#models for more information.
@@ -86,7 +86,7 @@ assembly:
     # assemblers used for shotgun sequencing with on Ion Torrent technology
     shotgun: "megahit-std"
     # assemblers used for amplicon sequencing with on Torrent technology
-    amplicon: "spades"
+    amplicon: "megahit-std"
   # minimum posterior probability for a clonal variant to be included in the generated pseudo-assembly
   min-variant-prob: 0.95
 

diff --git a/workflow/envs/varlociraptor.yaml b/workflow/envs/varlociraptor.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - varlociraptor =6.0
+  - varlociraptor =8.4