Merge pull request #66 from bcbio/fix_63_58_rnaseq

Fix 63 58 rnaseq

Author: lpantano

.github/workflows/R-CMD-check.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, devel]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, devel]
 
 name: R-CMD-check
 

inst/templates/rnaseq/00_libs/FA.R

@@ -3,14 +3,14 @@ library(clusterProfiler)
 source <- "https://github.com/bcbio/resources/raw/refs/heads/main/gene_sets/gene_sets/20240904"
 get_databases_v2=function(sps="human"){
   gmt.files=list(human=c("h.all.v2024.1.Hs.entrez.gmt",
-                         "c5.go.v2024.1.Hs.entrez.gmt",
+                         #"c5.go.v2024.1.Hs.entrez.gmt",
                          "c5.go.mf.v2024.1.Hs.entrez.gmt",
                          "c5.go.cc.v2024.1.Hs.entrez.gmt",
                          "c5.go.bp.v2024.1.Hs.entrez.gmt",
                          "c2.cp.reactome.v2024.1.Hs.entrez.gmt",
                          "c2.cp.kegg_legacy.v2024.1.Hs.entrez.gmt"),
                  mouse=c("mh.all.v2024.1.Mm.entrez.gmt",
-                         "m5.go.v2024.1.Mm.entrez.gmt",
+                         #"m5.go.v2024.1.Mm.entrez.gmt",
                          "m5.go.mf.v2024.1.Mm.entrez.gmt",
                          "m5.go.cc.v2024.1.Mm.entrez.gmt",
                          "m5.go.bp.v2024.1.Mm.entrez.gmt",

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{
@@ -59,22 +61,21 @@ load_metrics <- function(se_object, multiqc_data_dir, gtf_fn, counts){
                          package="bcbioR")
     }
     if (is.null(gtf)) {
-      print("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
+      warning("No genome provided! Please add it at the top of this Rmd")
     }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)]

inst/templates/rnaseq/01_quality_assesment/QC.Rmd

@@ -344,7 +344,7 @@ metrics %>%
 
 There should be little bias, i.e. the values should be close to 1, or at least consistent among samples
 
-```{r plot_53_bias}
+```{r plot_53_bias, eval=!all(is.na((metrics['r_and_t_rna_rate'])))}
 metrics %>%
   ggplot(aes(x = factor(sample, level = order),
              y = x5_3_bias, 

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

inst/templates/rnaseq/02_differential_expression/DEG.Rmd

@@ -682,12 +682,15 @@ if (!is.null(subset_value) & !is.null(subset_value)){
 } else {
   filenames = "full"
 }
+
+filename = paste0(filenames)
+name_expression_fn=file.path(
+  basedir,
+  str_interp("${filename}_expression.csv"))
+write_csv(counts_norm, name_expression_fn)
+
 for (contrast in names(contrasts)){
-  filename = paste0(filenames, "_", contrast)
-  name_expression_fn=file.path(
-    basedir,
-    str_interp("${filename}_expression.csv"))
-  
+
   name_deg_fn=file.path(
     basedir,
     str_interp("${filename}_deg.csv"))
@@ -708,7 +711,6 @@ for (contrast in names(contrasts)){
   pathways_for_writing <- fa_list[[contrast]][["all"]] %>% 
     mutate(comparison = contrast)
   
-  write_csv(counts_norm, name_expression_fn)
   write_csv(res_for_writing, name_deg_fn)
   write_csv(pathways_for_writing, name_pathways_fn)
 }