Convert a samplesheet CSV to SDRF (Sample and Data Relationship Format) TSV.
GENERATESDRFFROMSAMPLESHEET converts a simple CSV samplesheet into an SDRF-proteomics TSV file using the generate_sdrf.py script.
It takes pipeline parameters as a JSON string to populate SDRF columns including organism, enzyme, modifications, and other experiment-level metadata.
Used at the entry point of the main workflow when the user provides a samplesheet instead of a pre-built SDRF file.
| Channel | Type | Description |
|---|---|---|
| samplesheet | path | Input samplesheet CSV with columns: sample, spectra, condition (and optional label, fraction, replicate) |
| params_json | val(string) | Pipeline parameters as JSON string containing experiment-level parameters |
| Channel | Type | Description |
|---|---|---|
| sdrf | path | Generated SDRF-proteomics file (*.sdrf.tsv) |
| versions | path | Software versions (versions.yml) |
| Parameter | Default | Description |
|---|---|---|
| ext.args | '' | Additional CLI arguments appended to the generate_sdrf.py command |
community.wave.seqera.io/library/python:3.12.13--27a817c2c0890658
Used in the main workflow (workflows/msproteomics.nf) to generate SDRF files from user-provided samplesheets.
This enables users to provide a simple CSV format instead of the full SDRF specification.