This function resumes a FLAMES pipeline by running configured but unfinished steps.
See also
run_FLAMES to run the entire pipeline.
Examples
pipeline <- example_pipeline("BulkPipeline")
#> Writing configuration parameters to: /tmp/RtmpdufN84/file7a181724bef4/config_file_31256.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 @ Tue Aug 19 07:47:16 2025 ───────────────────
#> Creating junction bed file from GFF3 annotation.
#> Aligning sample sample1 -> /tmp/RtmpdufN84/file7a181724bef4/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/RtmpdufN84/file7a181724bef4/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/RtmpdufN84/file7a181724bef4/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
pipeline <- resume_FLAMES(pipeline)
#> Resuming pipeline from step: isoform_identification
#> ── Running step: isoform_identification @ Tue Aug 19 07:47:16 2025 ─────────────
#> ── Running step: read_realignment @ Tue Aug 19 07:47:17 2025 ───────────────────
#> Realigning sample sample1 -> /tmp/RtmpdufN84/file7a181724bef4/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/RtmpdufN84/file7a181724bef4/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/RtmpdufN84/file7a181724bef4/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 @ Tue Aug 19 07:47:17 2025 ──────────