Introduction
This document describes output produced by the pipeline. All paths below are relative to --outdir unless noted otherwise.
Pipeline overview
The pipeline is built using Nextflow and processes data using the following steps:
- BUSCO results - Per-lineage packaged BUSCO outputs
- MultiQC - Aggregate report describing results and QC from the whole pipeline
- Pipeline information - Report metrics generated during the workflow execution
BUSCO results
Output files
busco/
<lineage>/
<sample_prefix>.short_summary.tsv<sample_prefix>.short_summary.txt<sample_prefix>.short_summary.json<sample_prefix>.full_table.tsv.gz<sample_prefix>.missing_busco_list.tsv.gz<sample_prefix>.single_copy_busco_sequences.tar.gz<sample_prefix>.multi_copy_busco_sequences.tar.gz<sample_prefix>.fragmented_busco_sequences.tar.gz
Per-row outdir values in the samplesheet change where busco/ is published:
- relative
outdir: <global_outdir>/<row_outdir>/busco/...
- absolute
outdir: <row_outdir>/busco/...
Output files
busco/<lineage>/<sample_prefix>.short_summary.tsv<sample_prefix>.short_summary.txt<sample_prefix>.short_summary.json<sample_prefix>.full_table.tsv.gz<sample_prefix>.missing_busco_list.tsv.gz<sample_prefix>.single_copy_busco_sequences.tar.gz<sample_prefix>.multi_copy_busco_sequences.tar.gz<sample_prefix>.fragmented_busco_sequences.tar.gz
Per-row outdir values in the samplesheet change where busco/ is published:
- relative
outdir:<global_outdir>/<row_outdir>/busco/... - absolute
outdir:<row_outdir>/busco/...
The pipeline runs BUSCO for each selected lineage/ODB combination and then restructures outputs into a lineage-first hierarchy, with compressed tables and sequence bundles.
MultiQC
Output files
multiqc_report.html: standalone report at top-level outdir.
Output files
multiqc_report.html: standalone report at top-level outdir.
MultiQC summarises pipeline parameters and software versions generated during the run.
Pipeline information
Output files
pipeline_info/
- Reports generated by Nextflow:
execution_report_<timestamp>.html, execution_timeline_<timestamp>.html, execution_trace_<timestamp>.txt, pipeline_dag_<timestamp>.html.
- Software versions collected by the pipeline:
busco_software_mqc_versions.yml.
- Parameters used by the pipeline run:
params.json.
Output files
pipeline_info/- Reports generated by Nextflow:
execution_report_<timestamp>.html,execution_timeline_<timestamp>.html,execution_trace_<timestamp>.txt,pipeline_dag_<timestamp>.html. - Software versions collected by the pipeline:
busco_software_mqc_versions.yml. - Parameters used by the pipeline run:
params.json.
- Reports generated by Nextflow:
Nextflow provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.