fixed ci tests

Author: SusiJo

tests/test_tools.yml

@@ -438,6 +438,27 @@
     - path: results/variant_calling/sample2/mutect2/sample2.filtered.vcf.gz.filteringStats.tsv
     - path: results/csv/variantcalled.csv
 
+- name: Run variant calling on somatic sample with mutect2
+  command: nextflow run main.nf -profile test,tools_somatic,docker --tools mutect2 -c ./tests/nextflow.config
+  tags:
+    - mutect2_manual
+    - manual
+    - somatic
+    - variant_calling
+  files:
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.vcf.gz.stats
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.contamination.table
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.segmentation.table
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample3.pileupsummaries.table
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4.pileupsummaries.table
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.artifactprior.tar.gz
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.filtered.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.filtered.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.filtered.vcf.gz.filteringStats.tsv
+    - path: results/csv/variantcalled.csv
+
 - name: Run variant calling on somatic sample with msisensor-pro
   command: nextflow run main.nf -profile test,tools_somatic,docker --tools msisensorpro
   tags:

tests/test_tools_manually.yml

@@ -23,27 +23,6 @@
     - path: results/variant_calling/sample4_vs_sample3/ascat/Tumour.rawprofile.png
     - path: results/variant_calling/sample4_vs_sample3/ascat/Tumour.sunrise.png
 
-- name: Run variant calling on somatic sample with mutect2
-  command: nextflow run main.nf -profile test,tools_somatic,docker --tools mutect2 -c ./tests/nextflow.config
-  tags:
-    - mutect2_manual
-    - manual
-    - somatic
-    - variant_calling
-  files:
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.vcf.gz.stats
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.contamination.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.segmentation.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample3.pileupsummaries.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4.pileupsummaries.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.artifactprior.tar.gz
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.filtered.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.filtered.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.filtered.vcf.gz.filteringStats.tsv
-    - path: results/csv/variantcalled.csv
-
 - name: Run variant calling on somatic sample with mutect2 without intervals
   command: nextflow run main.nf -profile test,tools_somatic,docker --tools mutect2 --no_intervals -c ./tests/nextflow.config
   tags: