Accessing and reviewing outputs

Accessing workflow outputs

RAFT stores workflow outputs under each project’s outputs/ directory. Most sample-level and patient-level files are written under outputs/samples/.

Output categories

RAFT outputs usually fall into three broad categories:

  • outputs/samples/ contains sample-level, pair-level, and patient-level workflow outputs

  • outputs/reports/ contains workflow execution reports such as Nextflow reports, traces, and timelines

  • outputs/qc/ contains quality-control summaries and related metrics when a workflow generates them

If you are looking for biological results, start with outputs/samples/. If you are trying to understand what ran, how long each step took, or whether a step failed, check outputs/reports/ and the project’s logs/ directory.

The directory structure is organized hierarchically by dataset, patient, run, and tool:

Hierarchy of RAFT sample outputs

For example, a project with two patients might look like this:

Example RAFT outputs directory tree

How output names map to the manifest

RAFT uses manifest fields to organize outputs. In general:

  • dataset directories come from the manifest Dataset column

  • patient directories come from the manifest Patient_Name column

  • run directories come from the manifest Run_Name column

Some workflows also create combined run directories such as ad-123+nd-234. These represent outputs generated from paired or grouped inputs rather than from a single run alone.

Finding specific outputs

The fastest way to find a specific file type is usually the find command. For example, to list all VCF files produced by a project:

$ find /path/to/raft/projects/<PROJECT_ID>/outputs -name "*vcf*"

To list all BAM files produced by a project:

$ find /path/to/raft/projects/<PROJECT_ID>/outputs -name "*.bam"

To list workflow execution reports:

$ find /path/to/raft/projects/<PROJECT_ID>/outputs/reports -maxdepth 1 -type f

To list QC-related files:

$ find /path/to/raft/projects/<PROJECT_ID>/outputs -path "*/qc/*"

If you want to copy all VCF files from a project for downstream analysis:

$ find /path/to/raft/projects/<PROJECT_ID>/outputs -name "*vcf*" -exec cp {} /path/to/destination\;

The find manual page is available in the Linux man pages.

Note

Each project’s outputs/ directory lives inside the project directory: /path/to/raft/projects/<PROJECT_ID>/outputs.

For more information about the organization of outputs/, see Outputs.

Reviewing results

RAFT provides a web-based interface to review sample-level statistics and perform quality control checks. This interface is available by running:

$ raft generate-reports --project-id <PROJECT_ID>
RAFT generate-reports viewer

The RAFT generate-reports viewer.

Note

A demonstration report is available by either running raft generate-reports --demo or visiting the hosted demo report page.

Troubleshooting missing outputs

If you do not see the outputs you expect:

  • Check outputs/reports/ for workflow execution reports

  • Check the project’s logs/ directory for task logs and Nextflow output

  • Confirm that the relevant workflow step actually ran

  • Verify that you are looking under the correct dataset, patient, or run name from your manifest