nf-core_modules/tests/modules/gatk4/markduplicatesspark/nextflow.config

process {

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

    withName: GATK4_MARKDUPLICATES_SPARK_METRICS {
        ext.args = '--metrics-file test.metrics'
    }
}
// override tests/config/nextflow.config
docker.userEmulation = false
Improve syntax/logic coherence in all gatk4 plugins (#1459) * feat: code polishing * Apply suggestions from code review Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * code polishing * more code polishing * code polishing * tests for applybqsrspark * fix typo * no need to check md5sum for versions.yml * fix: use correct syntax * code polishing again * add tests for markduplicatesspark * simplify mergevcfs tests * add tests for baserecalibratorspark * fix: path to entry * code polishing * fix linting * simplify module * update meta.yml * fix pair mode * fix: MITO mode * more tests * fix command * bad copy paste * fix typos * fix tests * fix test * update meta.yml * correct versions.yml in all test.yml * code polishing * code polishing * more code polishing * fix args * add tmpdir for all Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> 2022-04-12 15:15:39 +00:00			`process {`

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

added test for metrics 2022-05-31 12:35:29 +00:00			`withName: GATK4_MARKDUPLICATES_SPARK_METRICS {`
			`ext.args = '--metrics-file test.metrics'`
			`}`
Improve syntax/logic coherence in all gatk4 plugins (#1459) * feat: code polishing * Apply suggestions from code review Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * code polishing * more code polishing * code polishing * tests for applybqsrspark * fix typo * no need to check md5sum for versions.yml * fix: use correct syntax * code polishing again * add tests for markduplicatesspark * simplify mergevcfs tests * add tests for baserecalibratorspark * fix: path to entry * code polishing * fix linting * simplify module * update meta.yml * fix pair mode * fix: MITO mode * more tests * fix command * bad copy paste * fix typos * fix tests * fix test * update meta.yml * correct versions.yml in all test.yml * code polishing * code polishing * more code polishing * fix args * add tmpdir for all Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> 2022-04-12 15:15:39 +00:00			`}`
added test for metrics 2022-05-31 12:35:29 +00:00			`// override tests/config/nextflow.config`
override userEmulation 2022-05-25 14:37:44 +00:00			`docker.userEmulation = false`