Execute a single step of the FLAMES pipeline

This function runs the specified step of the FLAMES pipeline.

Usage

run_step(pipeline, step)

# S4 method for class 'FLAMES.Pipeline'
run_step(pipeline, step)

Arguments

pipeline

A FLAMES.Pipeline object.

step

The step to run. One of "barcode_demultiplex", "genome_alignment", "gene_quantification", "isoform_identification", "read_realignment", or "transcript_quantification".

Value

An updated FLAMES.Pipeline object.

See also

run_FLAMES to run the entire pipeline. resume_FLAMES to resume a pipeline from the last completed step.

Examples

pipeline <- example_pipeline("BulkPipeline")
#> Writing configuration parameters to:  /tmp/RtmpgpEV0i/file25bf266516d6/config_file_9663.json 
#> Configured steps: 
#> 	genome_alignment: TRUE
#> 	isoform_identification: TRUE
#> 	read_realignment: TRUE
#> 	transcript_quantification: TRUE
#> samtools not found, will use Rsamtools package instead
pipeline <- run_step(pipeline, "genome_alignment")
#> Running step: genome_alignment
#> Creating junction bed file from GFF3 annotation.
#> Aligning sample sample1 -> /tmp/RtmpgpEV0i/file25bf266516d6/sample1_align2genome.bam
#> Warning: samtools not found, using Rsamtools instead, this could be slower and might fail for large BAM files.
#> Sorting BAM files by genome coordinates with 1 threads...
#> Indexing bam files
#> Aligning sample sample2 -> /tmp/RtmpgpEV0i/file25bf266516d6/sample2_align2genome.bam
#> Warning: samtools not found, using Rsamtools instead, this could be slower and might fail for large BAM files.
#> Sorting BAM files by genome coordinates with 1 threads...
#> Indexing bam files
#> Aligning sample sample3 -> /tmp/RtmpgpEV0i/file25bf266516d6/sample3_align2genome.bam
#> Warning: samtools not found, using Rsamtools instead, this could be slower and might fail for large BAM files.
#> Sorting BAM files by genome coordinates with 1 threads...
#> Indexing bam files