Hi Sam! I've not heard people reporting this issue specifically to RGI (ampcombi might have an issue with this in some cases, but still being investigated). Given

--clean

is a native parameter of RGI, we would be happy to add this as a pipeline level parameter (it would be easy to implement as you see below) - please could you make an issue on GitHub) Otherwise, to implement what I would do in the pipeline code itself anyway: as a temporary work around you can manually add

--clean

yourself to the args2. Make a cusotmn config file (e.g.

custom.conf

) with the code block below and supply this to the

nextflow run

command with

-c custom.conf

.

process {
    withName: RGI_MAIN {
        publishDir = [
            [
                path: { "${params.outdir}/arg/rgi/${meta.id}" },
                mode: params.publish_dir_mode,
                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
                pattern: "*.{txt}",
            ],
            [
                path: { "${params.outdir}/arg/rgi/${meta.id}" },
                mode: params.publish_dir_mode,
                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
                pattern: "*.{json}",
                enabled: params.arg_rgi_savejson,
            ],
            [
                path: { "${params.outdir}/arg/rgi/${meta.id}/" },
                mode: params.publish_dir_mode,
                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
                pattern: "*temp*",
                enabled: params.arg_rgi_savetmpfiles,
            ],
        ]
        ext.args2  = [
            "--alignment_tool ${params.arg_rgi_alignmenttool}",
            "--data ${params.arg_rgi_data}",
            params.arg_rgi_includeloose ? '--include_loose' : '',
            params.arg_rgi_includenudge ? '--include_nudge' : '',
            params.arg_rgi_lowquality ? '--low_quality' : '',
            params.arg_rgi_split_prodigal_jobs ? '--split_prodigal_jobs' : '',
            "--clean",
        ].join(' ').trim()
    }
}