https://github.com/biosustain/dsp_nf-msdap
Nextflow pipeline for MS-DAP, a downstream pipeline to generate statistical reports for MS data
https://github.com/biosustain/dsp_nf-msdap
downstream-analysis nextflow-pipeline proteomics
Last synced: 23 days ago
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Nextflow pipeline for MS-DAP, a downstream pipeline to generate statistical reports for MS data
- Host: GitHub
- URL: https://github.com/biosustain/dsp_nf-msdap
- Owner: biosustain
- License: gpl-3.0
- Created: 2023-08-24T07:53:07.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2024-05-31T11:36:18.000Z (about 2 years ago)
- Last Synced: 2025-01-15T06:20:14.369Z (over 1 year ago)
- Topics: downstream-analysis, nextflow-pipeline, proteomics
- Language: R
- Homepage:
- Size: 165 KB
- Stars: 0
- Watchers: 5
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# dsp_nf-msdap
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