bowtie2.nf.test

nextflow_pipeline {

    name "Test pipeline with bowtie2 aligner"
    script "../main.nf"
    tag "bowtie2"

    test("bowtie2") {

        when {
            params {
                outdir = "$outputDir"
                aligner = "bowtie2"
            }
        }

        then {
            // stable_name: All files + folders in ${params.outdir}/ with a stable name
            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
            // stable_path: All files in ${params.outdir}/ with stable content
            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
            assertAll(
                { assert workflow.success },
                { assert snapshot(
                    // Number of successful tasks
                    workflow.trace.succeeded().size(),
                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_chipseq_software_mqc_versions.yml"),
                    // All stable path name, with a relative path
                    stable_name,
                    // All files with stable contents
                    stable_path
                ).match() }
            )
        }
    }

    test("bowtie2 with stub") {

        options "-stub"

        when {
            params {
                outdir = "$outputDir"
                aligner = "bowtie2"
            }
        }

        then {
            assertAll(
                { assert workflow.success },
                { assert snapshot(
                    workflow.trace.succeeded().size()
                ).match() }
            )
        }
    }
}