Merge pull request #172 from bcgsc/release/v8.1.0

Release/v8.1.0

.github/workflows/npm-test.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        node: ['12', '14', '16']
+        node: [16, 18, 20]
     name: node-${{ matrix.node }}
     steps:
       - uses: actions/checkout@v2

Snakefile

@@ -144,7 +144,7 @@ rule download_cgi:
     output: f'{DATA_DIR}/cgi/cgi_biomarkers_per_variant.tsv'
     shell: dedent(f'''\
         cd {DATA_DIR}/cgi
-        wget https://www.cancergenomeinterpreter.org/data/cgi_biomarkers_20180117.zip
+        wget https://www.cancergenomeinterpreter.org/data/biomarkers/cgi_biomarkers_20180117.zip
         unzip cgi_biomarkers_20180117.zip
         ''')
 
@@ -162,7 +162,7 @@ rule download_cancerhotspots:
     shell: dedent(f'''\
         mkdir -p {DATA_DIR}/cancerhotspots
         cd {DATA_DIR}/cancerhotspots
-        wget http://download.cbioportal.org/cancerhotspots/cancerhotspots.v2.maf.gz
+        wget https://cbioportal-download.s3.amazonaws.com/cancerhotspots.v2.maf.gz
         gunzip cancerhotspots.v2.maf.gz
         ''')
 
@@ -222,6 +222,7 @@ rule load_ncit:
 
 rule load_fda_srs:
     input: expand(rules.load_local.output, local=['vocab']),
+        f'{DATA_DIR}/ncit.COMPLETE',
         data=f'{DATA_DIR}/fda/UNII_Records.txt'
     container: CONTAINER
     log: f'{LOGS_DIR}/fdaSrs.logs.txt'

bin/load.js

@@ -109,6 +109,16 @@ civicParser.add_argument('--noUpdate', {
     default: false,
     help: 'Will not check for updating content of existing GraphKB Statements',
 });
+civicParser.add_argument('--noDeleteOnUnmatched', {
+    action: 'store_true',
+    default: false,
+    help: 'Will not delete GraphKB Statements from valid sourceID but not matching a combination',
+});
+civicParser.add_argument('--deleteDeprecated', {
+    action: 'store_true',
+    default: false,
+    help: 'Will delete GraphKB Statements from deprecated sourceID',
+});
 
 const clinicaltrialsgovParser = subparsers.add_parser('clinicaltrialsgov');
 clinicaltrialsgovParser.add_argument('--days', {

data/chromosomes.json

@@ -91,15 +91,18 @@
         },
         "MT": {
             "biotype": "chromosome",
-            "name": "chrMT"
+            "name": "chrMT",
+            "displayName":"mt"
         },
         "X": {
             "biotype": "chromosome",
-            "name": "chrX"
+            "name": "chrX",
+            "displayName":"x"
         },
         "Y": {
             "biotype": "chromosome",
-            "name": "chrY"
+            "name": "chrY",
+            "displayName":"y"
         }
     },
     "sources": {