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