Esearch input (#47) #106
Workflow file for this run
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| on: | |
| push: | |
| branches: [master, dev, validate-taxonomy] | |
| name: Validate taxonomy | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ['ubuntu-20.04' ] | |
| perl: [ '5.32' ] | |
| name: Perl ${{ matrix.perl }} on ${{ matrix.os }} | |
| steps: | |
| - name: Set up perl | |
| uses: shogo82148/actions-setup-perl@v1 | |
| with: | |
| perl-version: ${{ matrix.perl }} | |
| multi-thread: "true" | |
| - name: checkout my repo | |
| uses: actions/checkout@v4 | |
| with: | |
| path: Kalamari | |
| - name: update PATH | |
| run: | | |
| echo $GITHUB_WORKSPACE/Kalamari/bin >> $GITHUB_PATH | |
| echo $PATH | |
| echo "" | |
| cat $GITHUB_PATH | |
| - name: build taxonomy | |
| run: | | |
| echo $PATH | |
| bash Kalamari/bin/buildTaxonomy.sh | |
| bash Kalamari/bin/filterTaxonomy.sh | |
| ls -lhR Kalamari/share/kalamari-*/taxonomy | |
| - name: validate taxonomy | |
| run: | | |
| perl Kalamari/bin/validateTaxonomy.pl Kalamari/share/kalamari-*/taxonomy | |
| - name: validate filtered taxonomy | |
| run: | | |
| perl Kalamari/bin/validateTaxonomy.pl Kalamari/share/kalamari-*/taxonomy/filtered | |
| - name: matching taxids | |
| run: | | |
| export taxdir=$(\ls -d Kalamari/share/kalamari-*/taxonomy) | |
| echo "Making sure that all taxids in chromosomes.tsv and plasmids.tsv are present in nodes.tsv and names.tsv" | |
| tail -n +2 Kalamari/src/chromosomes.tsv Kalamari/src/plasmids.tsv -q | perl -F'\t' -lane 'BEGIN{@node=`cat $ENV{taxdir}/nodes.dmp`; for $n(@node){($taxid)=split(/\t/, $n); $taxid{$taxid}++; } } for my $t($F[2], $F[3]){ if(!$taxid{$t}){ print "Could not find $t taxid";} }' | |
| tail -n +2 Kalamari/src/chromosomes.tsv Kalamari/src/plasmids.tsv -q | perl -F'\t' -lane 'BEGIN{@name=`cat $ENV{taxdir}/names.dmp`; for $n(@name){($taxid)=split(/\t/, $n); $taxid{$taxid}++; } } for my $t($F[2], $F[3]){ if(!$taxid{$t}){ print "Could not find $t taxid";} }' |