Proteome CLI flags of epaa and nextflow differ

[jonasscheid]

Description of the bug

The epaa.py script expects a --reference_proteome as argument, however via the nextflow script only --proteome is parsed:

epitopeprediction/modules/local/epytope_peptide_prediction.nf

Line 24 in b0f0d7a

if (params.proteome) {

epaa.py: error: unrecognized arguments: --proteome /path/to/UP000005640_9606.fasta

Command used and terminal output

nextflow run nf-core/epitopeprediction -r dev  -profile cfc \
    --input samplesheet.csv \
    --outdir "filtered_out_all_proteome" \
    --filter_self \
    --proteome "path/to/UP000005640_9606.fasta" \
    --tools "syfpeithi,netmhc-4.0,netmhcpan-4.1,netmhciipan-4.1" \
    --netmhc_path /path/to/netMHC-4.0a.Linux.tar.gz \
    --netmhcpan_path /path/to/netMHCpan-4.1b.Linux.tar.gz \
    --netmhciipan_path /path/to/netMHCIIpan-4.1a.Linux.tar.gz \
    -resume

Relevant files

No response

System information

No response

[jonasscheid]

I checked the functionality of filtering out peptides that are in the human proteome and it doesn't work. I find peptides in the results that are substrings of the HP I provided. I used the test_full dataset

[christopher-mohr]

I checked the functionality of filtering out peptides that are in the human proteome and it doesn't work. I find peptides in the results that are substrings of the HP I provided. I used the test_full dataset

I guess it would be better to create a separate issue for that and maybe even in the epytope repository. Do you have a minimal example and could check if you can reproduce it with this epytope version and the most recent one?