Fast-forward merge

R/BLAZE_demultiplexing.R

@@ -22,7 +22,7 @@
 #' fastq1 <- bfc[[names(BiocFileCache::bfcadd(bfc, 'Fastq1', fastq1_url))]]
 #' outdir <- tempfile()
 #' dir.create(outdir)
-#' config = jsonlite::fromJSON(system.file('extdata/blaze_flames.json', package = 'FLAMES'))
+#' config = jsonlite::fromJSON(system.file('extdata/template_config.json', package = 'FLAMES'))
 #' config$blaze_parameters['output-prefix'] <- outdir
 #' \dontrun{
 #'    blaze(config$blaze_parameters, fastq1)

R/minimap2_align.R

@@ -260,20 +260,17 @@ locate_minimap2_dir <- function(minimap2_dir = NULL) {
 }
 
 locate_samtools <- function() {
-  which_samtools <- base::system2(command="command", args=c("-v", "samtools"));
+  which_samtools <- base::system2(command = "command", args = c("-v", "samtools"))
   if (which_samtools == 0) {
     return(
-      dirname(
-        base::system2(
-          command="command", 
-          args=c("-v", "samtools"),
-          stderr=TRUE, stdout=TRUE
-        )
+      base::system2(
+        command = "command",
+        args = c("-v", "samtools"),
+        stderr = TRUE, stdout = TRUE
       )
     )
-  } 
-
-  return(FALSE);
+  }
+  return(FALSE)
 }
 
 # total mapped primary secondary

R/sc_long_multisample_pipeline.R

@@ -259,7 +259,11 @@ sc_long_multisample_pipeline <-
         # realign to transcript
         if (config$pipeline_parameters$do_read_realignment) {
             cat("#### Realign to transcript using minimap2\n")
-            infqs_realign <- file.path(outdir, paste(samples, "matched_reads_dedup.fastq", sep = "_"))
+            if (config$pipeline_parameters$do_gene_quantification) { 
+                infqs_realign <- file.path(outdir, paste(samples, "matched_reads_dedup.fastq", sep = "_"))
+            } else {
+                infqs_realign <- infqs
+            }
             for (i in 1:length(samples)) {
                 cat(paste0(c("\tRealigning sample ", samples[i], "...\n")))
                 minimap2_realign(config, infqs_realign[i], outdir, minimap2_dir, prefix = samples[i], 

R/sc_long_pipeline.R

@@ -252,7 +252,11 @@ sc_long_pipeline <-
         # realign to transcript
         if (config$pipeline_parameters$do_read_realignment) {
             cat("#### Realigning deduplicated reads to transcript using minimap2\n")
-            infq_realign <- file.path(outdir, "matched_reads_dedup.fastq")
+            if (config$pipeline_parameters$do_gene_quantification) {
+                infq_realign <- file.path(outdir, "matched_reads_dedup.fastq")
+            } else {
+                infq_realign <- infq
+            }
             minimap2_realign(config, infq_realign, outdir, minimap2_dir, prefix = NULL, 
                              threads = config$pipeline_parameters$threads)
         } else {

vignettes/FLAMES_vignette.Rmd

@@ -28,7 +28,7 @@ This R package was created to simplify installation and execution of the FLAMES
 knitr::include_graphics(system.file("images/FLAMESpipeline-01.png", package = "FLAMES"))
 ```
 
-Input to FLAMES are fastq files generated from the long-read platform. Using a cell barcode allow-list (e.g. barcode list obtained from short-read sequencing), the `find_barcode()` function locates the barcode sequencing in the long-reads and trims the cell barcodes and the flanking UMI sequence. The pipeline then calls `minimap_align()`, a `minimap2` wrapper, to align the demultiplex long-reads to the reference genome. Next, `find_isoform()` is called to identify novel isoforms using the alignment, creating an updated transcript assembly. The demultiplexed reads are then aligned to the transcript assembly by the function `minimap_realign()`. Finally, FLAMES calls `quantify()` to quantify the transcript counts using the (re-)alignment file.
+Input to FLAMES are fastq files generated from the long-read platform. Using a cell barcode allow-list (e.g. barcode list obtained from short-read sequencing), the `find_barcode()` function locates the barcode sequencing in the long-reads and trims the cell barcodes and the flanking UMI sequence. The pipeline then calls `minimap_align()`, a `minimap2` wrapper, to align the demultiplex long-reads to the reference genome. Next, `find_isoform()` is called to identify novel isoforms using the alignment, creating an updated transcript assembly. The demultiplexed reads are then aligned to the transcript assembly by the function `minimap_realign()`. Finally, FLAMES calls `quantify_transcript()` to quantify the transcript counts using the (re-)alignment file.
 
 Figure \@ref(fig:workflow) summerise the steps of the pipeline described above. The pipeline functions (`sc_long_pipeline`, `bulk_long_pipeline`, `sc_long_multisample_pipline`) execute the steps sequentially and return `SingleCellExperiment` object, `SummarizedExperiment` object and a list of `SingleCellExperiment` objects respectivly. 
 
@@ -112,7 +112,7 @@ if (is.character(minimap2_dir)) { # do not run if minimap2 cannot be found
     config = config, fq_in = fastq,
     outdir = outdir, minimap2_dir = minimap2_dir
   )
-  quantify(annotation = annot, outdir = outdir, config = config)
+  quantify_transcript(annotation = annot, outdir = outdir, config = config)
   sce <- create_sce_from_dir(outdir = outdir, annotation = annot)
 }
 ```