Example pipelins

Provides example pipelines for bulk, single cell and multi-sample single cell.

Usage

example_pipeline(type = "SingleCellPipeline", outdir)

Arguments

type

The type of pipeline to create. Options are "SingleCellPipeline", "BulkPipeline", and "MultiSampleSCPipeline".

outdir

(Optional) The output directory where the example pipeline will be created. If not provided, a temporary directory will be created.

Value

A pipeline object of the specified type.

See also

SingleCellPipeline for creating the single cell pipeline, BulkPipeline for bulk long data, MultiSampleSCPipeline for multi sample single cell pipelines.

Examples

example_pipeline("SingleCellPipeline")
#> Writing configuration parameters to:  /tmp/RtmpA5lNG6/file329034736ffa/config_file_12944.json 
#> Configured steps: 
#> 	barcode_demultiplex: TRUE
#> 	genome_alignment: TRUE
#> 	gene_quantification: TRUE
#> 	isoform_identification: TRUE
#> 	read_realignment: TRUE
#> 	transcript_quantification: TRUE
#> samtools not found, will use Rsamtools package instead
#> → A FLAMES.SingleCellPipeline outputting to /tmp/RtmpA5lNG6/file329034736ffa
#> 
#> ── Inputs 
#> ✔ fastq: ...ibrary/FLAMES/extdata/fastq/musc_rps24.fastq.gz
#> ✔ annotation: /__w/_temp/Library/FLAMES/extdata/rps24.gtf.gz
#> ✔ genome_fa: /tmp/RtmpA5lNG6/file329034736ffa/rps24.fa
#> ✔ barcodes_file: /tmp/RtmpA5lNG6/file329034736ffa/bc_allow.tsv
#> 
#> ── Outputs 
#> ℹ demultiplexed_fastq: matched_reads.fastq.gz
#> ℹ deduped_fastq: matched_reads_dedup.fastq.gz
#> ℹ genome_bam: align2genome.bam
#> ℹ transcriptome_assembly: transcript_assembly.fa
#> ℹ transcriptome_bam: realign2transcript.bam
#> 
#> ── Pipeline Steps 
#> ℹ barcode_demultiplex (pending)
#> ℹ genome_alignment (pending)
#> ℹ gene_quantification (pending)
#> ℹ isoform_identification (pending)
#> ℹ read_realignment (pending)
#> ℹ transcript_quantification (pending)