Last push did not include updated test scripts

TRON-Bioinformatics · Oct 10, 2023 · 16011f7 · 16011f7
1 parent ce941c1
commit 16011f7
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Showing 2 changed files with 6 additions and 5 deletions.
diff --git a/tests/scripts/test_15.sh b/tests/scripts/test_15.sh
@@ -9,12 +9,13 @@ source bin/assert.sh
 output=tests/output/test15
 nextflow main.nf -profile conda --name test_data \
 	--output $output \
-	--vcf $(pwd)/tests/test_data/test_data.lofreq.vcf \
-    --lineage_mode
+	--vcf $(pwd)/tests/test_data/test_data.assembly.lineage_mode.vcf.gz \
+        --lineage_mode \
+        --skip_normalization
 
 test -s $output/test_data.input.fasta || { echo "Missing VCF2FASTA fasta file (lineage mode with vcf input)!"; exit 1; }
 test -s $output/test_data.input.pangolin.csv || { echo "Missing pangolin output file (lineage mode with vcf input)!"; exit 1; }
-assert_eq $(wc -l $output/test_data.input.pangolin.csv) 2 "Wrong number of pangolin results"
+assert_eq $(wc -l $output/test_data.input.pangolin.csv | cut -d ' ' -f1) 2 "Wrong number of pangolin results"
 
 
 

diff --git a/tests/scripts/test_16.sh b/tests/scripts/test_16.sh
@@ -10,7 +10,7 @@ output=tests/output/test15
 nextflow main.nf -profile conda --name test_data \
 	--output $output \
 	--fasta $(pwd)/tests/test_data/test_data.fasta \
-    --lineage_mode
+    	--lineage_mode
 
 test -s $output/test_data.assembly.pangolin.csv || { echo "Missing pangolin output file (lineage mode with vcf input)!"; exit 1; }
-assert_eq $(wc -l $output/test_data.assembly.pangolin.csv) 2 "Wrong number of pangolin results"
+assert_eq $(wc -l $output/test_data.assembly.pangolin.csv | cut -d ' ' -f1) 2 "Wrong number of pangolin results"