Fix lints

uclahs-cds · Jul 29, 2024 · 8e10b3b · 8e10b3b
1 parent 5977e7e
commit 8e10b3b
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Showing 3 changed files with 3 additions and 4 deletions.
diff --git a/docker/install-stablelift.R b/docker/install-stablelift.R
@@ -1,12 +1,12 @@
 install.packages('renv', lib = .Library)
 
 options(
-    renv.settings.bioconductor.version = Sys.getenv("BIOC_VERSION")
+    renv.settings.bioconductor.version = Sys.getenv('BIOC_VERSION')
 )
 
 renv::init(
     bare = TRUE,
-    bioconductor = Sys.getenv("BIOC_VERSION")
+    bioconductor = Sys.getenv('BIOC_VERSION')
 )
 
 renv::install(c(

diff --git a/module/scripts/liftover-Delly2-vcf.R b/module/scripts/liftover-Delly2-vcf.R
@@ -151,7 +151,7 @@ for (i in seq_len(nrow(fix.lifted))) {
 output.vcf <- input.vcf;
 output.vcf@fix <- as.matrix(fix.lifted);
 output.vcf@gt <- as.matrix(gt.dt);
-output.vcf@meta <- output.vcf@meta[!grepl("^##(contig|reference)", output.vcf@meta)];
+output.vcf@meta <- output.vcf@meta[!grepl('^##(contig|reference)', output.vcf@meta)];
 output.vcf@meta <- c(output.vcf@meta, header.contigs);
 
 write.vcf(output.vcf, output);
diff --git a/module/scripts/predict-liftover-stability.R b/module/scripts/predict-liftover-stability.R
@@ -158,4 +158,3 @@ annotation.dt <- data.table(
     );
 sort.genomic.dt(annotation.dt);
 fwrite(annotation.dt, file = output.tsv, sep = '\t', col.names = FALSE);
-