## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
library(FLAMES)

## ----eval=TRUE, echo=TRUE-----------------------------------------------------
outdir <- tempfile()
dir.create(outdir)
# some example data
# known cell barcodes, e.g. from coupled short-read sequencing
bc_allow <- file.path(outdir, "bc_allow.tsv")
R.utils::gunzip(
  filename = system.file("extdata", "bc_allow.tsv.gz", package = "FLAMES"),
  destname = bc_allow, remove = FALSE
)
# reference genome
genome_fa <- file.path(outdir, "rps24.fa")
R.utils::gunzip(
  filename = system.file("extdata", "rps24.fa.gz", package = "FLAMES"),
  destname = genome_fa, remove = FALSE
)

pipeline <- SingleCellPipeline(
  # use the default configs
  config_file = create_config(outdir),
  outdir = outdir,
  # the input fastq file
  fastq = system.file("extdata", "fastq", "musc_rps24.fastq.gz", package = "FLAMES"),
  # reference annotation file
  annotation = system.file("extdata", "rps24.gtf.gz", package = "FLAMES"),
  genome_fa = genome_fa,
  barcodes_file = bc_allow
)
pipeline

## ----eval=TRUE, echo=TRUE-----------------------------------------------------
pipeline <- run_FLAMES(pipeline)
pipeline

## ----eval=TRUE, echo=TRUE-----------------------------------------------------
# set up a new pipeline
outdir2 <- tempfile()
pipeline2 <- SingleCellPipeline(
  config_file = create_config(outdir),
  outdir = outdir2,
  fastq = system.file("extdata", "fastq", "musc_rps24.fastq.gz", package = "FLAMES"),
  annotation = system.file("extdata", "rps24.gtf.gz", package = "FLAMES"),
  genome_fa = genome_fa,
  barcodes_file = bc_allow
)

# delete the reference genome
unlink(genome_fa)
pipeline2 <- run_FLAMES(pipeline2)
pipeline2

## ----eval=TRUE, echo=TRUE-----------------------------------------------------
R.utils::gunzip(
  filename = system.file("extdata", "rps24.fa.gz", package = "FLAMES"),
  destname = genome_fa, remove = FALSE
)
pipeline2 <- resume_FLAMES(pipeline2)
pipeline2

## ----eval=TRUE, echo=TRUE-----------------------------------------------------
experiment(pipeline)

## ----eval=TRUE, echo=TRUE-----------------------------------------------------
# example_pipeline provides an example pipeline for each of the three types
# of pipelines: BulkPipeline, SingleCellPipeline and MultiSampleSCPipeline
mspipeline <- example_pipeline("MultiSampleSCPipeline")

# don't have to run the entire pipeline for this
# let's just run the demultiplexing step
mspipeline <- run_step(mspipeline, "barcode_demultiplex")
plot_demultiplex(mspipeline)

## ----echo=FALSE---------------------------------------------------------------
utils::sessionInfo()