Merge pull request #237 from sigven/favicon

Use local favicon and remove system calls

conda/recipe/pcgrr/meta.yaml

@@ -26,6 +26,7 @@ requirements:
     - r-dplyr
     - r-dt
     - r-formattable
+    - r-fs
     - bioconductor-genomeinfodb
     - r-ggplot2
     - r-glue
@@ -61,6 +62,7 @@ requirements:
     - r-dplyr
     - r-dt
     - r-formattable
+    - r-fs
     - bioconductor-genomeinfodb
     - r-ggplot2
     - r-glue

pcgrr/DESCRIPTION

@@ -36,6 +36,7 @@ Imports:
     dplyr,
     DT,
     formattable,
+    fs,
     GenomeInfoDb,
     ggplot2,
     glue,

pcgrr/NAMESPACE

@@ -78,7 +78,6 @@ export(log4r_warn)
 export(log_var_eitem_stats)
 export(make_cnaqc_object)
 export(max_af_gnomad)
-export(mkdir)
 export(msi_indel_fraction_plot)
 export(msi_indel_load_plot)
 export(order_variants)

pcgrr/R/main.R

@@ -929,17 +929,17 @@ write_report_quarto_html <- function(report = NULL){
           output_dir,
           paste0('quarto_', stringi::stri_rand_strings(1, 15))
         )
+        fs::dir_create(tmp_quarto_dir)
         quarto_main_template <-
-          glue::glue("{tmp_quarto_dir}{.Platform$file.sep}pcgr_quarto_report.qmd")
+          file.path(tmp_quarto_dir, "pcgr_quarto_report.qmd")
         quarto_main_template_sample <-
-          glue::glue("{tmp_quarto_dir}{.Platform$file.sep}pcgr_quarto_report_sample.qmd")
+          file.path(tmp_quarto_dir, "pcgr_quarto_report_sample.qmd")
         quarto_html <-
-          glue::glue("{tmp_quarto_dir}{.Platform$file.sep}pcgr_quarto_report_sample.html")
+          file.path(tmp_quarto_dir, "pcgr_quarto_report_sample.html")
 
         ## Copy all PCGR quarto reporting templates, bibliography, css etc to
         ## the temporary directory for quarto report rendering
-        invisible(pcgrr::mkdir(tmp_quarto_dir))
-        system(glue::glue("cp -r {pcgr_rep_template_path}{.Platform$file.sep}* {tmp_quarto_dir}"))
+        fs::dir_copy(pcgr_rep_template_path, tmp_quarto_dir)
 
         ## Save sample PCGR report object in temporary quarto rendering directory
         rds_report_path <- file.path(
@@ -977,17 +977,14 @@ write_report_quarto_html <- function(report = NULL){
         ## Copy output HTML report from temporary rendering directory
         ## to designated HTML file in output directory
         if(file.exists(quarto_html)){
-          system(
-            glue::glue(paste0(
-              "cp -f {quarto_html} ",
-              "{fnames[['html']]}")))
+          fs::file_copy(quarto_html, fnames[["html"]])
         }else{
           cat("WARNING\n")
         }
 
         ## remove temporary quarto directory (if debugging is switched off)
         if(!(settings$conf$debug)){
-          system(glue::glue("rm -rf {tmp_quarto_dir}"))
+          fs::dir_delete(tmp_quarto_dir)
         }
         #pcgrr::log4r_info("------")
       }

pcgrr/R/mutational_signatures.R

@@ -494,7 +494,7 @@ generate_report_data_signatures <-
       }
     }
 
-    system(glue::glue("rm -f {vcf_name_mutsig_analysis}*"))
+    fs::file_delete(glue::glue("{vcf_name_mutsig_analysis}.gz"))
 
     return(pcg_report_signatures)
   }

pcgrr/R/utils.R

@@ -878,7 +878,7 @@ write_processed_vcf <- function(calls,
   system(paste0("bgzip -f ", vcf_fname))
   system(paste0("tabix -p vcf ", vcf_fname, ".gz"))
 
-  system(paste0("rm -f ", sample_vcf_content_fname))
+  fs::file_delete(sample_vcf_content_fname)
 }
 
 
@@ -1023,20 +1023,6 @@ check_file_exists <- function(fname) {
   }
 }
 
-
-#' Create directory
-#'
-#' @param d Directory to create.
-#'
-#' @export
-mkdir <- function(d) {
-  if (!dir.exists(d)) {
-    dir.create(d, recursive = TRUE)
-  }
-  TRUE
-}
-
-
 #' Strip HTML tags
 #'
 #' Remove HTML tags and comments from text.

pcgrr/inst/templates/pcgr_quarto_report.qmd

@@ -8,7 +8,7 @@ title-block-banner-color: "white"
 linkcolor: '#0073C2'
 include-in-header:
   - text: |
-      <link rel="shortcut icon" href="https://github.com/sigven/pcgr/raw/master/pcgrr/pkgdown/favicon/favicon-16x16.png" />
+      <link rel="shortcut icon" href="favicon-16x16.png" />
       <style>
       .panel-tabset > .tab-content {
         border: none;