deps: update Nextclade to newer (lenient) version 2.4.x

RIVM-bioinformatics · Aug 11, 2022 · d5b90e2 · d5b90e2
1 parent 8a8059e
commit d5b90e2
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diff --git a/SARS2seq/workflow/envs/Typing.yaml b/SARS2seq/workflow/envs/Typing.yaml
@@ -9,7 +9,7 @@ dependencies:
   - python=3.7
   - libffi==3.3
   - pangolin==4.0.2
-  - nextclade=1.10
+  - nextclade=2.4
   - snakemake<=6.8.0
   - pandas==1.3.5
   - usher

diff --git a/SARS2seq/workflow/workflow.smk b/SARS2seq/workflow/workflow.smk
@@ -963,8 +963,8 @@ rule Typing:
     shell:
         """
         nextclade run \
+            {input.fasta} \
             --input-dataset '{input.nc_dataset}' \
-            --input-fasta '{input.fasta}' \
             --output-csv '{output.nextc}' > {log} 2>&1
         pangolin \
             {input.fasta} \