Outputs

RAFT outputs are available in a project’s outputs/ directory. The outputs/ directory can contain a variety of subdirectories but generally includes at least qc/, reports/, and samples/.

reports/

The reports/ directory contains reports generated by Nextflow:

• dag.dot - A directed acyclic graph dot file that can be used to understand the flow among processes. The .dot file can be converted to a graph using graphviz.

• report.html - A report with a wealth of information regarding each process run by the workflow. Useful for understanding resource limitations within the workflow.

• timeline.html - A report showing a graphical representation of each process’s run time.

• trace.txt - A text file containing information about each process run. Useful for troubleshooting as grep can be used to find specific processes. This file exists within the project’s log/ directory while the workflow is running.

Hierarchical Output Directory Structure

Directories containing sample-level outputs (qc/ and samples/) follow:

samples/
  \__<DATASET>
        \__<PAT_NAME>
              \__<RUN_NAME>

Therefore, samples outputs are defined by the Dataset, Pat_Name, and Run_Name columns from the user-provided manifest.

Some situations, like variant calling, may involve multiple samples from the same patient. In this case, the <RUN_NAME>/ directory is defined as <RUN_NAME_1>_<RUN_NAME2>/.

samples/

Sample-level outputs can be found within the samples/ directory. Outputs are partitioned by sample where appropriate. For example, the outputs for samples ar-279 for patient Pt01 in datasets Foo_2024 can be found in outputs/samples/Foo_2024/Pt01/ar-279/.

ls samples/Foo_2024/Pt01/ar-279/
fastp
salmon_aln_quant
samtools_coverage
seq2hla
seqtk_subseq
starfusion

Each subdirectory, (e.g. starfusion/) contains symbolic links to the output files contained within the project’s work/ dirctory.

qc/

Quality control data for each sample can be found in the qc/ directory. These outputs are generally tool-level reported metrics.