8a78f2f53d1ee8640a4f326765646466b5dcfa5b
angie
  Fri Aug 26 11:43:56 2022 -0700
Updating usage for latest version of nextclade.

diff --git src/hg/utils/otto/sarscov2phylo/runNextclade.sh src/hg/utils/otto/sarscov2phylo/runNextclade.sh
index d91c158..c49c2ea 100755
--- src/hg/utils/otto/sarscov2phylo/runNextclade.sh
+++ src/hg/utils/otto/sarscov2phylo/runNextclade.sh
@@ -10,31 +10,25 @@
 
 xcat () {
   for f in $@; do
     if [ "${f##*.}" == "xz" ]; then
         xzcat $f
     elif [ "${f##*.}" == "gz" ]; then
         zcat $f
     else
         cat $f
     fi
   done
 }
 export -f xcat
 
 logfile=$(mktemp)
-outDir=$(mktemp -d)
 
 nDataDir=~angie/github/nextclade/data/sars-cov-2
-nextclade run -i <(xcat $faIn | sed -re 's@^>hCo[Vv]-19/+@>@;  s/[ '"'"',()]//g;') \
+nextclade run <(xcat $faIn | sed -re 's@^>hCo[Vv]-19/+@>@;  s/[ '"'"',()]//g;') \
     --input-dataset $nDataDir \
-    --output-dir $outDir \
-    --output-tsv $outBase.nextclade.full.tsv \
-    --output-basename out \
+    --output-tsv $outBase.nextclade.full.tsv.gz \
+    --output-fasta $outBase.nextalign.fasta.xz \
     --jobs 1 \
     >& $logfile
 
-gzip -f $outBase.nextclade.full.tsv
-xz -f $outDir/out.aligned.fasta
-cp -p $outDir/out.aligned.fasta.xz $outBase.nextalign.fasta.xz
-
 rm -rf $logfile $outDir