Outputs

RAFT writes workflow results under each project’s outputs/ directory. This page focuses on the technical structure of that directory and how it relates to the project’s work/ and logs/ directories.

Output categories

Most projects include at least these subdirectories:

  • outputs/samples/: biological outputs organized by dataset, patient, and run

  • outputs/qc/: quality-control outputs organized using the same hierarchy

  • outputs/reports/: Nextflow execution reports such as DAGs, traces, and timelines

outputs/reports/

The reports/ directory contains workflow-level execution reports generated by Nextflow. Common files include:

  • dag.dot: directed acyclic graph description of the workflow

  • report.html: run summary with process-level resource and execution details

  • timeline.html: graphical timeline of process execution

  • trace.txt: tabular process-level execution log

During execution, some report files may first appear under the project’s logs/ directory and then be copied or linked into outputs/reports/ when the run completes.

Hierarchical output structure

Sample-level outputs under samples/ and qc/ follow the same basic hierarchy:

outputs/
  samples/
    <DATASET>/
      <PATIENT_NAME>/
        <RUN_NAME>/
  qc/
    <DATASET>/
      <PATIENT_NAME>/
        <RUN_NAME>/

These names come from the manifest:

  • Dataset defines <DATASET>

  • Patient_Name defines <PATIENT_NAME>

  • Run_Name defines <RUN_NAME>

Some workflows also create combined run directories for grouped analyses. For example, a tumor-normal pair may be represented as ad-Pt01+nd-Pt01.

samples/

The samples/ directory contains analysis outputs intended for downstream biological interpretation.

For example, the outputs for run ar-279 from patient Pt01 in dataset Foo_2024 would typically live under:

outputs/samples/Foo_2024/Pt01/ar-279/

A run directory usually contains one subdirectory per tool or task, for example:

fastp/
salmon_aln_quant/
samtools_coverage/
seq2hla/
seqtk_subseq/
starfusion/

In many workflows, these files are symbolic links back into the project’s work/ directory rather than independent copies. That keeps outputs organized without duplicating large intermediate files unnecessarily.

qc/

The qc/ directory contains tool-reported QC metrics and summaries. These files follow the same dataset/patient/run hierarchy as samples/.

For example:

outputs/qc/Foo_2024/Pt01/ad-Pt01-pre/
  fastp/
  multiqc/
  samtools_coverage/

These QC outputs are what raft generate-reports reads when building the browser-based review interface.

Relationship to work/ and logs/

outputs/ is the organized results view of a project. It is not the same as the Nextflow work/ directory.

  • work/ contains task working directories and intermediate execution files

  • outputs/ contains organized result files and links intended for review and downstream use

  • logs/ contains Nextflow logs and related execution metadata

If you are troubleshooting a failed task, start in logs/ and work/. If you are looking for final workflow results, start in outputs/.