fix expected test outputs

Author: maxulysse

tests/test_annotation.yml

@@ -4,17 +4,17 @@
     - annotation
     - snpeff
   files:
-    - path: results/variant_annotation/GM12878/GM12878.haplotypecaller.filtered_snpEff.ann.vcf.gz
-    - path: results/variant_annotation/GM12878/GM12878.haplotypecaller.filtered_snpEff.ann.vcf.gz.tbi
+    - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_snpEff.ann.vcf.gz
+    - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_snpEff.ann.vcf.gz.tbi
     - path: results/reports/multiqc_report.html
 - name: Run VEP
   command: nextflow run main.nf -profile test,docker --annotate_tools vep --skip_multiqc --outdir results --download_cache
   tags:
     - annotation
     - vep
   files:
-    - path: results/variant_annotation/GM12878/GM12878.haplotypecaller.filtered_VEP.ann.vcf.gz
-    - path: results/variant_annotation/GM12878/GM12878.haplotypecaller.filtered_VEP.ann.vcf.gz.tbi
+    - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_VEP.ann.vcf.gz
+    - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_VEP.ann.vcf.gz.tbi
 - name: Run snpEff followed by VEP
   command: nextflow run main.nf -profile test,docker --annotate_tools merge --skip_multiqc --outdir results --download_cache
   tags:
@@ -23,5 +23,5 @@
     - snpeff
     - vep
   files:
-    - path: results/variant_annotation/GM12878/GM12878.haplotypecaller.filtered_snpEff_VEP.ann.vcf.gz
-    - path: results/variant_annotation/GM12878/GM12878.haplotypecaller.filtered_snpEff_VEP.ann.vcf.gz.tbi
+    - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_snpEff_VEP.ann.vcf.gz
+    - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_snpEff_VEP.ann.vcf.gz.tbi