This function runs the specified step of the FLAMES pipeline.
Usage
run_step(pipeline, step, disable_controller = TRUE)
# S4 method for class 'FLAMES.Pipeline'
run_step(pipeline, step, disable_controller = TRUE)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".
- disable_controller
(optional) If TRUE, the step will be executed in the current R session, instead of using crew controllers.
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/RtmpA5lNG6/file3290550105ac/config_file_12944.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 @ Mon Jun 23 02:42:34 2025 ───────────────────
#> Creating junction bed file from GFF3 annotation.
#> Aligning sample sample1 -> /tmp/RtmpA5lNG6/file3290550105ac/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/RtmpA5lNG6/file3290550105ac/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/RtmpA5lNG6/file3290550105ac/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