nf-core_modules/tests/modules/panaroo/run/nextflow.config

process {

    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }

    withName: PANAROO_RUN {
        ext.args = '--clean-mode strict -a core'
    }
}
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version 2022-03-25 02:11:04 +00:00			`process {`

			`publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }`

			`withName: PANAROO_RUN {`
			`ext.args = '--clean-mode strict -a core'`
			`}`
			`}`