chord cli: bsgenome required beforehand

umccr · Dec 15, 2024 · 58faee4 · 58faee4
1 parent 004cb52
commit 58faee4
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diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
@@ -4,7 +4,7 @@ on:
   push:
     branches:
       - main
-      - gha-test
+      - docker_update
 env:
   atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }}
   recipe_path: conda/recipe

diff --git a/inst/cli/chord.R b/inst/cli/chord.R
@@ -8,6 +8,8 @@ chord_add_args <- function(subp) {
 
 chord_parse_args <- function(args) {
   cli::cli_h1("Started running CHORD!")
+  # CHORD requires this to be loaded...
+  suppressPackageStartupMessages(library("BSgenome.Hsapiens.UCSC.hg38"))
   res <- sigrap::chord_run(
     vcf.snv = args$snv, vcf.sv = args$sv,
     sample.name = args$sample, outpath = args$out