Updated path in test_14.sh

TRON-Bioinformatics · Oct 5, 2023 · 5e90601 · 5e90601
1 parent 7b0482e
commit 5e90601
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/tests/scripts/test_14.sh b/tests/scripts/test_14.sh
@@ -9,8 +9,8 @@ output=tests/output/test14
 nextflow main.nf -profile conda --name test_data \
 	--output $output \
 	--reference_generate \
-    --reference reference/Sars_cov_2.ASM985889v3.dna.toplevel.fa  \
-    --gff reference/Sars_cov_2.ASM985889v3.101.gff3 \
+    --reference $(pwd)/reference/Sars_cov_2.ASM985889v3.dna.toplevel.fa  \
+    --gff $(pwd)/reference/Sars_cov_2.ASM985889v3.101.gff3 \
     --snpeff_organism Sars_cov_2
 
 # Test reference genome related output

diff --git a/tests/scripts/test_15.sh b/tests/scripts/test_15.sh
@@ -9,7 +9,7 @@ source bin/assert.sh
 output=tests/output/test15
 nextflow main.nf -profile conda --name test_data \
 	--output $output \
-	--vcf tests/test_data/test_data.lofreq.vcf \
+	--vcf $(pwd)/tests/test_data/test_data.lofreq.vcf \
     --lineage_mode
 
 test -s $output/test_data.input.fasta || { echo "Missing VCF2FASTA fasta file (lineage mode with vcf input)!"; exit 1; }

diff --git a/tests/scripts/test_16.sh b/tests/scripts/test_16.sh
@@ -9,7 +9,7 @@ source bin/assert.sh
 output=tests/output/test15
 nextflow main.nf -profile conda --name test_data \
 	--output $output \
-	--fasta tests/test_data/test_data.fasta \
+	--fasta $(pwd)/tests/test_data/test_data.fasta \
     --lineage_mode
 
 test -s $output/test_data.assembly.pangolin.csv || { echo "Missing pangolin output file (lineage mode with vcf input)!"; exit 1; }