From 19a6d6428a9fc43f42f15d2f4c3bdb76117ed429 Mon Sep 17 00:00:00 2001 From: pdimens Date: Mon, 29 Apr 2024 09:58:34 -0400 Subject: [PATCH] rm guardrails --- src/harpy/reports/Leviathan.Rmd | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/harpy/reports/Leviathan.Rmd b/src/harpy/reports/Leviathan.Rmd index 29b1d81ef..64bd46518 100644 --- a/src/harpy/reports/Leviathan.Rmd +++ b/src/harpy/reports/Leviathan.Rmd @@ -42,8 +42,8 @@ script src = "https://ajax.googleapis.com/ajax/libs/jquery/3.7.1/jquery.min.js" ## Intro ### introtext {.no-title} ```{r} -#statsfile <- snakemake@input[["statsfile"]] -statsfile <- "/home/pdimens/Documents/harpy/SV/leviathanpop/reports/data/pop1.sv.stats" +statsfile <- snakemake@input[["statsfile"]] +#statsfile <- "/home/pdimens/Documents/harpy/SV/leviathanpop/reports/data/pop1.sv.stats" samplename <- gsub(".sv.stats", "", basename(statsfile)) ``` @@ -80,8 +80,8 @@ if (nrow(sv) == 0) { } ``` ```{r contigSizes, echo = FALSE} -#faidx <- snakemake@input[["faidx"]] -faidx <- "/home/pdimens/Documents/harpy/Genome/genome.fasta.fai" +faidx <- snakemake@input[["faidx"]] +#faidx <- "/home/pdimens/Documents/harpy/Genome/genome.fasta.fai" fa.sizes <- read.table(faidx, header = F)[,1:2] %>% arrange(desc(2)) colnames(fa.sizes) <- c("contig", "size")