Identifies mzML using Comet, returns PSMs in TSV format, calculates the FDR and filters them.
conda env create -f environment.yml
conda activate comet_ident
Hint: Will only install Python 3 and Pandas from the requirements file for now. If those dependencies are installed on your system anyway, you may skip this.
- Prepare your mzMLs e.g. by converting RAW-files etc, and put them in a folder
- Prepare the comet settings
comet -pwill create a well documented default parameter filecomet.params.new- Adjust them to your needs
- The workflow only need Comet's txt-output, and makes sure it is active. Everything else can be disabled.
- Run the workflow
nextflow run comet_ident.nf <ARGUMENTS>
| Argument | Description |
|---|---|
| --comet-bin | Path to comet binary |
| --comet-params | Path to comet parameter file |
| --fasta | Path to target/decoy FASTA |
| --mzml-dir | Path to mzML dir |
| --results-dir | Path to results dir |
| --fdr-threshold | Threshold for FDR |
| --keep-decoys | If not 0, decoys will be removed from filtered PSMs, default 0 |
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