Updated pangolin recipe

Author: fredericlemoine

pangolin/v4.3.1-v1.23.1-v0.3.19-v0.1.12/Dockerfile

@@ -18,13 +18,16 @@ RUN apk update \
     && pip install --upgrade cryptography \
     && pip install pyOpenSSL \
     && conda update conda \
+    && conda update --all \
     && conda install mamba -c conda-forge
 
+COPY pangolin.patch /
 
 RUN cd / \
     && git clone https://github.com/cov-lineages/pangolin.git \
     && cd pangolin \
     && git checkout $VERSION \
+    && git apply /pangolin.patch \
     && cd .. \
     && sed -i 's/name: pangolin/name: base/' /pangolin/environment.yml \
     && sed -i s=git+https://github.com/cov-lineages/pangolin-data.git=git+https://github.com/cov-lineages/pangolin-data.git@$DATAVERSION= /pangolin/environment.yml \

pangolin/v4.3.1-v1.23.1-v0.3.19-v0.1.12/pangolin.patch

@@ -0,0 +1,12 @@
+diff --git a/pangolin/scripts/usher.smk b/pangolin/scripts/usher.smk
+index 3adffc7..3ba0938 100644
+--- a/pangolin/scripts/usher.smk
++++ b/pangolin/scripts/usher.smk
+@@ -106,6 +106,7 @@ rule usher_inference:
+                 echo ""
+             fi
+             cat {input.fasta:q} >> {params.ref_fa:q}
++            sed -i 's/^ *//' {params.ref_fa:q}
+             faToVcf -includeNoAltN {params.ref_fa:q} {params.vcf:q}
+             $usher -n -D -i {input.usher_protobuf:q} -v {params.vcf:q} -T $threads -d '{config[tempdir]}' &> {log}
+         else