This function creates a horizontal bar plot showing the duration of each pipeline step using ggplot2.
Examples
pipeline <- example_pipeline("BulkPipeline")
#> Writing configuration parameters to: /tmp/RtmpyvgB0f/file76e35a8def5d/config_file_30435.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 @ Mon Aug 25 09:35:30 2025 ───────────────────
#> Creating junction bed file from GFF3 annotation.
#> Aligning sample sample1 -> /tmp/RtmpyvgB0f/file76e35a8def5d/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/RtmpyvgB0f/file76e35a8def5d/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/RtmpyvgB0f/file76e35a8def5d/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 @ Mon Aug 25 09:35:31 2025 ─────────────
#> ── Running step: read_realignment @ Mon Aug 25 09:35:31 2025 ───────────────────
#> Realigning sample sample1 -> /tmp/RtmpyvgB0f/file76e35a8def5d/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/RtmpyvgB0f/file76e35a8def5d/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/RtmpyvgB0f/file76e35a8def5d/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 @ Mon Aug 25 09:35:32 2025 ──────────
plot_durations(pipeline)
