Fixed two more tests (#41)

* update yml * query fallback * debugging msg * fix path to taxonomydb * print first two lines of fasta files * helpful cut statement * remove head statement in last step
lskatz · May 8, 2024 · 29f3439 · 29f3439
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commit 29f3439
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diff --git a/.github/workflows/unit-testing.Yersinia.Kraken2.yml b/.github/workflows/unit-testing.Yersinia.Kraken2.yml
@@ -47,7 +47,10 @@ jobs:
       - name: download
         run:  perl Kalamari/bin/downloadKalamari.pl --outdir ${{ matrix.GENUS }} ${{ env.TSV }}
       - name: check-results
-        run:  tree ${{ matrix.GENUS }}
+        run:  |
+          tree ${{ matrix.GENUS }}
+          echo "First two lines of each fasta file:"
+          find ${{ matrix.GENUS }} -name '*.fasta' | xargs head -n 2 | cut -c 1-60
       - name: install kraken
         run:  |
           wget https://github.com/DerrickWood/kraken2/archive/refs/tags/v2.1.2.tar.gz -O kraken-v2.1.2.tar.gz
@@ -77,8 +80,7 @@ jobs:
           ls -lhSR ${{ env.DB }}
           QUERY=$(find ${{ matrix.GENUS }} -name '*.fasta' | head -n 1)
           echo "QUERY is $QUERY"
-          head -n 2 $QUERY
-          kraken2 --db ${{ env.DB }} --report kraken2.report --use-mpa-style --output kraken2.raw $QUERY
+          set -x; kraken2 --db ${{ env.DB }} --report kraken2.report --use-mpa-style --output kraken2.raw $QUERY; set +x;
           head kraken2.report kraken2.raw
 
 
diff --git a/.github/workflows/validateTaxonomy.yml b/.github/workflows/validateTaxonomy.yml
@@ -37,6 +37,7 @@ jobs:
       #    perl Kalamari/bin/validateTaxonomy.pl Kalamari/share/kalamari-*/taxonomy/nodes.dmp Kalamari/share/kalamari-*/taxonomy/names.dmp
       - 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 Kalamari/src/taxonomy/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 Kalamari/src/taxonomy/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";} }'
+          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";} }'