Steps to perform in the pipeline
Value
A named logical vector containing all possible steps for the pipeline. The names of the vector are the step names, and the values are logical indicating whether the step is configured to be performed.
Examples
ppl <- example_pipeline()
#> Writing configuration parameters to: /tmp/RtmpgpEV0i/file25bf5650f66e/config_file_9663.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
steps(ppl)
#> barcode_demultiplex genome_alignment gene_quantification
#> TRUE TRUE TRUE
#> isoform_identification read_realignment transcript_quantification
#> TRUE TRUE TRUE