Nextflow pipeline for MS-DAP, a downstream pipeline to generate statistical PDF reports for MS data
This repository aims to serve as a headless launcher for msdap - https://github.com/biosustain/msdap
This very early development verion is only compatible with Spectronaut output, but all formats supported by msdap will be compatible with the final version.
to generate a pdf report with MS-DAP, the following are needed:
- Mass Spec report as would be needed for MS DAP.
- Fasta file with proteome / TAXID for species to autodownload from Uniprot.
- ordered list of replicate group names.
The enviromnent running this script will need following dependencies:
- Nextflow
- Docker with min 16 gb of ram for the R installation with MS-DAP
- python3 with pandas
Example to initiate this pipeline (9606 indicates that proteome for human will be downloaded):
./nextflow run flow_main.nf ## nexflow workflow file
--library reference ## Directory where the reference proteomes and fasta files should be found/downloaded
--force.download False ## Whether to force download of fasta file
--taxid 9606 ## NCBI Taxonomic identifier of studied organism
--file [full_path]/data/DIA_Report.csv ## Processed proteomics file (e.g., output spectronaut)
--groups [full_path]/data/groups.xlsx ## File specifying conditions to be contrasted
--format spectronaut ## Format of the proteomics file
content of groups.xlsx:
sample_id / group
Attributions: Metromap adapted in part with remixed components from nf-co.re/sarek