Testing different Feature Finding Algorithms for UnbeQuant

This is a simple workflow, which utilizes different feature finders and reports the number of identified/unidentified Features/MS2s and also how many of the MS2s have been associated with a feature. Additionally some plots are generated.

The workflow provides two importable workflows and can be easily extended to more FeatureFinders if needed.

How to run

For running this worklfow, make sure, nextflow and docker is available and simply run:

nextflow run main.nf -resume --main_fasta_file "path_to_fasta" --main_comet_params "path_to_comet_config" --main_raw_files_folder "path_to_d_and_raw_files"

This workflows uses the unbequant:1:0 docker which can be built locally here: UnbeQuant.

Additonal parameters which may need adjusting, depending on the input files:

--
--charge_low "Number"  // Lowest allowed Charge for a feature
--charge_high "Number"  // Highest allowed Charge for a feature
--ppm_tolerance "Number"  // Set to the same tolerance, as used for identification
--rt_enlarge_factor "Decimal"  // Allowed error in Retention Time

In main.nf a brief description for every parameter is provided.