This function creates a horizontal bar plot showing the duration of each pipeline step using ggplot2.
Examples
pipeline <- example_pipeline("BulkPipeline")
#> ℹ Writing configuration to: /tmp/Rtmp4nGYdi/filebc447a45d33f/config_file_48196.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_FLAMES(pipeline)
#> ── Running step: genome_alignment @ Fri Jun 26 08:24:58 2026 ───────────────────
#> Creating junction bed file from GFF3 annotation.
#> Aligning sample sample1 -> /tmp/Rtmp4nGYdi/filebc447a45d33f/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/Rtmp4nGYdi/filebc447a45d33f/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/Rtmp4nGYdi/filebc447a45d33f/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
#> ── Running step: isoform_identification @ Fri Jun 26 08:25:00 2026 ─────────────
#> ── Running step: read_realignment @ Fri Jun 26 08:25:00 2026 ───────────────────
#> Realigning sample sample1 -> /tmp/Rtmp4nGYdi/filebc447a45d33f/sample1_realign2transcript.bam
#> Warning: samtools not found, using Rsamtools instead, this could be slower and might fail for large BAM files.
#> Skipped sorting BAM files.
#> Realigning sample sample2 -> /tmp/Rtmp4nGYdi/filebc447a45d33f/sample2_realign2transcript.bam
#> Warning: samtools not found, using Rsamtools instead, this could be slower and might fail for large BAM files.
#> Skipped sorting BAM files.
#> Realigning sample sample3 -> /tmp/Rtmp4nGYdi/filebc447a45d33f/sample3_realign2transcript.bam
#> Warning: samtools not found, using Rsamtools instead, this could be slower and might fail for large BAM files.
#> Skipped sorting BAM files.
#> ── Running step: transcript_quantification @ Fri Jun 26 08:25:01 2026 ──────────
plot_durations(pipeline)
