Leafcutter BAM to Junctions
| Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
|---|---|---|---|
| aou_9.0.0 | July, 2025 | WARP Pipelines | File an issue |
Introduction to the Leafcutter BAM to Junctions workflow
leafcutter_bam_to_junc.wdl defines workflow leafcutter_bam_to_junc_workflow, which extracts splice junctions from BAM inputs for sQTL processing.
Reads are filtered for mapping quality and WASP tags, then regtools junctions extract produces compressed junction outputs per sample.
Inputs
Input descriptions
| Input variable name | Description | Type |
|---|---|---|
bam_file | Input aligned BAM file. | File |
sample_id | Sample identifier used in output naming. | String |
strand_specificity | (Optional) strand-specificity setting for regtools (0 default). | Int? |
user_defined_threads | (Optional) thread override (default 1). | Int? |
user_defined_preempt | (Optional) preemptible count override (default 1). | Int? |
Outputs
| Output variable name | Filename, if applicable | Output format and description |
|---|---|---|
junc_file_final | <sample_id>.regtools_junc.txt.gz | Gzipped splice junction file extracted from filtered BAM reads. |
pipeline_version_out | aou_9.0.0 | Workflow version string output. |
Workflow and WDL
- Workflow:
leafcutter_bam_to_junc_workflow - Source WDL:
leafcutter_bam_to_junc.wdl
Versioning
All leafcutter_bam_to_junc releases are documented in the changelog.
Feedback
Please help us make our tools better by filing an issue in WARP; we welcome pipeline-related suggestions or questions.