Info about used software (e.g. environment.yml, Dockerfile): https://github.com/nf-core/proteomicslfq
Instructions:
- Install Java 8+
- Install docker or singularity
- Install nextflow (
wget -qO- https://get.nextflow.io | bash
) - ~/nextflow run nf-core/proteomicslfq -r dev -profile docker --input https://raw.githubusercontent.com/bigbio/proteomics-metadata-standard/master/annotated-projects/PXD001819/PXD001819.sdrf.tsv --database https://raw.githubusercontent.com/nf-core/test-datasets/proteomicslfq/testdata-aws/uniprot\_yeast\_reviewed\_isoforms\_ups1\_crap.fasta\_td.fasta -with-report -with-trace -with-timeline
Results:
- MSstats folder contains final results/quants post-processed by MSstats
- openms_msstats-ready_out.csv contains the raw aggregated intensities