Issue with the process: EXTERNAL_TOOLS_IMPORT

[marissaDubbelaar]

Description of the bug

There seems to be an error when the netmhcpan version 4.0 is used.
I checked the ~/.nextflow/assets/nf-core/epitopeprediction/assets/external_tools_meta.json and this seems to be in there. Maybe the issue can be easily resolved?

"netmhcpan_darwin": {
        "4.0": {
            "version": 4.0,
            "software_md5": "042d16b89adcf5656ca4deae06b55cc6",
            "data_url": "https://services.healthtech.dtu.dk/services/NetMHCpan-4.0/data.Darwin.tar.gz",
            "data_md5": "b4eef3c82852d677a98e0f7d753a36e2",
            "binary_name": "netMHCpan"
        },
        "4.1": {
            "version": 4.0,
            "software_md5": "5f6eab43feb80a24e32eb02b22e9db5f",
            "data_url": "https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/data.tar.gz",
            "data_md5": "4bdd3944cb4c5b8ba4d8900dae074c85",
            "binary_name": "netMHCpan"
        }
    },

Command used and terminal output

nextflow run nf-core/epitopeprediction --input input.csv -profile docker --max_memory 4.GB --max_cpus 4 --min_peptide_length 8 --max_peptide_length 12 --outdir ./ligandomat_results --netmhcpan_path /Users/dubbelaar/lib/netMHCpan-4.1b.Darwin.tar.gz

Relevant files

nextflow.log

System information

• Nextflow version 22.10.1
• Hardware: MacBook
• Executor: local
• Container engine: Docker
• OS: macOS
• Version of nf-core/epitopeprediction: 2.1.0

[christopher-mohr]

Hi Marissa, thanks for the report. I assume you also added netmhcpan-4.1 to the --tools parameter value? Could you please try adding --netmhc_system darwin?

[marissaDubbelaar]

oops yes the --tools parameter included syfpeithi,netmhcpan-4.1. I just tested it out at it seems to work.
Thank you @christopher-mohr, close the issue if you like. But I was wondering maybe good to alter the version under netmhcpan_darwin, 4.0?

[christopher-mohr]

oops yes the --tools parameter included syfpeithi,netmhcpan-4.1. I just tested it out at it seems to work.
Thank you @christopher-mohr, close the issue if you like. But I was wondering maybe good to alter the version under netmhcpan_darwin, 4.0?

Yes, I noticed that as well, I will fix it in the next PR. Thanks!