From 8e10b3bb52c24a6678a4cb56b1cf5dec1d41ac6c Mon Sep 17 00:00:00 2001 From: Nicholas Wiltsie Date: Mon, 29 Jul 2024 12:26:08 -0700 Subject: [PATCH] Fix lints --- docker/install-stablelift.R | 4 ++-- module/scripts/liftover-Delly2-vcf.R | 2 +- module/scripts/predict-liftover-stability.R | 1 - 3 files changed, 3 insertions(+), 4 deletions(-) diff --git a/docker/install-stablelift.R b/docker/install-stablelift.R index f5543bb..ef50338 100644 --- 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 index 827a3b1..d473091 100644 --- 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 index 4962f4f..7f3f90a 100644 --- 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); -