A related question, what determines the output structure in a pipeline Result section on the nf-core website? The outputs for the 2.2.0 release are a bit of a mess and I’d like to avoid losing the expected output structure if possible

In general, if all works as intended, the AWS folder in the website should contain everything you publish in the specified --outdir

Really helpful to know! I suspect something didn’t go right with the past runs, this is the expected output (this time for the simulated data rather than HCC1395 data):

output/
├── pipeline_info
│   ├── execution_report_2025-11-27_02-39-19.html
│   ├── execution_timeline_2025-11-27_02-39-19.html
│   ├── execution_trace_2025-11-27_02-39-19.txt
│   ├── params_2025-11-27_02-39-53.json
│   ├── pipeline_dag_2025-11-27_02-39-19.html
│   └── software_versions.yml
└── subject_a
    ├── alignments
    ├── amber
    ├── bamtools
    ├── chord
    ├── cider
    ├── cobalt
    ├── cuppa
    ├── esvee
    ├── isofox
    ├── lilac
    ├── linx
    ├── logs
    ├── neo
    ├── orange
    ├── pave
    ├── peach
    ├── purple
    ├── sage
    ├── sage_append
    ├── sigs
    ├── teal
    ├── virusbreakend
    └── virusinterpreter

Yes the website list lists the contents of the s3 bucket, it doesn't do anything more clever than that

Got it, thanks @Phil Ewels