rename filtered vcf

Author: lindaxiang

payload-gen-variant-filtering/main.py

@@ -48,7 +48,7 @@ def calculate_md5(file_path):
 def get_files_info(file_to_upload):
     basename = os.path.basename(file_to_upload)
     input_wf = basename.split(".")[5]
-    variant_type = basename.split(".")[8]
+    variant_type = basename.split(".")[7]
     file_info = {
         'fileName': basename,
         'fileType': 'VCF' if basename.endswith('.vcf.gz') else basename.split(".")[-1].upper(),

payload-gen-variant-filtering/tests/expected/expected.gatk-mutect2.filtered.snv.payload.json

@@ -26,7 +26,7 @@
   ],
   "files": [
     {
-      "fileName": "TEST-PR.DO250183.SA610229.wgs.20200922.gatk-mutect2.somatic.filtered.snv.vcf.gz",
+      "fileName": "TEST-PR.DO250183.SA610229.wgs.20200922.gatk-mutect2.somatic.snv.filtered.vcf.gz",
       "fileType": "VCF",
       "fileSize": 23947,
       "fileMd5sum": "1ebce71c8231aeb7ac6c06c92adfd5db",
@@ -41,7 +41,7 @@
       "dataType": "Raw SNV Calls"
     },
     {
-      "fileName": "TEST-PR.DO250183.SA610229.wgs.20200922.gatk-mutect2.somatic.filtered.snv.vcf.gz.tbi",
+      "fileName": "TEST-PR.DO250183.SA610229.wgs.20200922.gatk-mutect2.somatic.snv.filtered.vcf.gz.tbi",
       "fileType": "TBI",
       "fileSize": 185,
       "fileMd5sum": "7a8482dc43849a4ee8bdd4c9c77fae0c",

payload-gen-variant-filtering/tests/expected/expected.sanger-wgs.filtered.snv.payload.json

@@ -26,7 +26,7 @@
   ],
   "files": [
     {
-      "fileName": "TEST-PR.DO250183.SA610229.wgs.20200513.sanger-wgs.somatic.filtered.snv.vcf.gz",
+      "fileName": "TEST-PR.DO250183.SA610229.wgs.20200513.sanger-wgs.somatic.snv.filtered.vcf.gz",
       "fileType": "VCF",
       "fileSize": 23947,
       "fileMd5sum": "1ebce71c8231aeb7ac6c06c92adfd5db",
@@ -41,7 +41,7 @@
       "dataType": "Raw SNV Calls"
     },
     {
-      "fileName": "TEST-PR.DO250183.SA610229.wgs.20200513.sanger-wgs.somatic.filtered.snv.vcf.gz.tbi",
+      "fileName": "TEST-PR.DO250183.SA610229.wgs.20200513.sanger-wgs.somatic.snv.filtered.vcf.gz.tbi",
       "fileType": "TBI",
       "fileSize": 185,
       "fileMd5sum": "7a8482dc43849a4ee8bdd4c9c77fae0c",

payload-gen-variant-filtering/tests/expected/expected.sanger-wxs.filtered.indel.payload.json

@@ -26,7 +26,7 @@
   ],
   "files": [
     {
-      "fileName": "TEST-PR.DO250183.SA610229.wxs.20200911.sanger-wxs.somatic.filtered.indel.vcf.gz",
+      "fileName": "TEST-PR.DO250183.SA610229.wxs.20200911.sanger-wxs.somatic.indel.filtered.vcf.gz",
       "fileType": "VCF",
       "fileSize": 23947,
       "fileMd5sum": "1ebce71c8231aeb7ac6c06c92adfd5db",
@@ -41,7 +41,7 @@
       "dataType": "Raw InDel Calls"
     },
     {
-      "fileName": "TEST-PR.DO250183.SA610229.wxs.20200911.sanger-wxs.somatic.filtered.indel.vcf.gz.tbi",
+      "fileName": "TEST-PR.DO250183.SA610229.wxs.20200911.sanger-wxs.somatic.indel.filtered.vcf.gz.tbi",
       "fileType": "TBI",
       "fileSize": 185,
       "fileMd5sum": "7a8482dc43849a4ee8bdd4c9c77fae0c",