make rRNA optional when reading metrics

bcbio · Jan 15, 2025 · 349fc06 · 349fc06
1 parent 680df7c
commit 349fc06
Show file tree

Hide file tree

Showing 2 changed files with 19 additions and 16 deletions.
diff --git a/inst/templates/rnaseq/00_libs/load_data.R b/inst/templates/rnaseq/00_libs/load_data.R
@@ -44,6 +44,8 @@ load_metrics <- function(se_object, multiqc_data_dir, gtf_fn, counts){
 
     # Sometimes we don't have rRNA due to mismatch annotation, We skip this if is the case
     gtf <- NULL
+    biotype <- NULL
+
     if (genome =="other"){
       gtf <- gtf_fn
     }else{
@@ -60,20 +62,20 @@ load_metrics <- function(se_object, multiqc_data_dir, gtf_fn, counts){
     }
     if (is.null(gtf)) {
       warning("No genome provided! Please add it at the top of this Rmd")
-    }
-
-    gtf=rtracklayer::import(gtf)
-
-    one=grep("gene_type", colnames(as.data.frame(gtf)), value = TRUE)
-    another=grep("gene_biotype", colnames(as.data.frame(gtf)), value = TRUE)
-    biotype=NULL
-    if(length(one)==1){
-      biotype=one
-    }else if(length(another)==1){
-      biotype=another
     }else{
-      warning("No gene biotype founded")
+      gtf=rtracklayer::import(gtf)
+
+      one=grep("gene_type", colnames(as.data.frame(gtf)), value = TRUE)
+      another=grep("gene_biotype", colnames(as.data.frame(gtf)), value = TRUE)
+      if(length(one)==1){
+        biotype=one
+      }else if(length(another)==1){
+        biotype=another
+      }else{
+        warning("No gene biotype founded")
+      }
     }
+
     metrics$sample <- make.names(metrics$sample)
     if (!is.null(biotype)){
       annotation=as.data.frame(gtf) %>% .[,c("gene_id", biotype)]

diff --git a/inst/templates/rnaseq/01_quality_assesment/params_qc.R b/inst/templates/rnaseq/01_quality_assesment/params_qc.R
@@ -2,11 +2,12 @@
 
 # Your data
 # This is the file used to run nf-core or compatible to that
-coldata_fn='/Path/to/metadata/meta.csv'
+coldata_fn <- '/Path/to/metadata/meta.csv'
 # This file is inside star_salmon/ folder
-counts_fn='/path/to/nf-core/output/star_salmon/salmon.merged.gene_counts.tsv'
+counts_fn <- '/path/to/nf-core/output/star_salmon/salmon.merged.gene_counts.tsv'
 # This folder called "multiqc_report_data" is inside the output directory star_salmon inside multiqc folder
-multiqc_data_dir='/path/to/nf-core/output/multiqc/star_salmon/multiqc_report_data'
+multiqc_data_dir <- '/path/to/nf-core/output/multiqc/star_salmon/multiqc_report_data'
 # This file is inside the genome folder in the output directory, use this only for non-model organism
 # gtf_fn='/path/to/nf-core/output/genome/hg38.filtered.gtf'
-se_object = NA
+gtf_fn <- NULL
+se_object <-  NA