remove_ribo_rna.nf.test

nextflow_pipeline {

    name "Test pipeline with ribosomal RNA removal"
    script "../main.nf"
    tag "pipeline"
    tag "remove_ribo_rna"

    test("Params: --remove_ribo_rna") {

        when {
            params {
                outdir = "$outputDir"
                remove_ribo_rna = true
                // Skip processes already covered by default.nf.test (rRNA removal only affects read count, not BAM structure)
                skip_qc = true
                skip_stringtie = true
                skip_bigwig = true
            }
        }

        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 ${params.outdir}/ with stable content
            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
            assertAll(
                { assert workflow.success},
                { assert snapshot(
                    // Number of successful tasks
                    workflow.trace.succeeded().size(),
                    // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"),
                    // All stable path name, with a relative path
                    stable_name,
                    // All files with stable contents
                    stable_path
                ).match() }
            )
        }

        cleanup {
            // Only prune/delete on CI - keeping local VM state intact prevents
            // cross-test launchDir wipes that break nf-test snapshot walks.
            if (System.getenv("CI") == "true") {
                if (System.getenv("NFT_PROFILE")?.contains("docker")) {
                    "docker system prune -a -f --volumes".execute()
                }
                new File("${launchDir}").deleteDir()
            }
        }
    }

    test("Params: --remove_ribo_rna - stub") {

        options "-stub"

        when {
            params {
                outdir = "$outputDir"
                remove_ribo_rna = true
                // Skip processes already covered by default.nf.test (rRNA removal only affects read count, not BAM structure)
                skip_qc = true
                skip_stringtie = true
                skip_bigwig = true
            }
        }

        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 ${params.outdir}/ with stable content
            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
            assertAll(
                { assert workflow.success},
                { assert snapshot(
                    // Number of successful tasks
                    workflow.trace.succeeded().size(),
                    // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"),
                    // All stable path name, with a relative path
                    stable_name,
                    // All files with stable contents
                    stable_path
                ).match() }
            )
        }

        cleanup {
            // Only prune/delete on CI - keeping local VM state intact prevents
            // cross-test launchDir wipes that break nf-test snapshot walks.
            if (System.getenv("CI") == "true") {
                if (System.getenv("NFT_PROFILE")?.contains("docker")) {
                    "docker system prune -a -f --volumes".execute()
                }
                new File("${launchDir}").deleteDir()
            }
        }
    }

    test("Params: --remove_ribo_rna --ribo_removal_tool bowtie2") {

        when {
            params {
                outdir = "$outputDir"
                remove_ribo_rna = true
                ribo_removal_tool = 'bowtie2'
                // Skip processes already covered by default.nf.test (rRNA removal only affects read count, not BAM structure)
                skip_qc = true
                skip_stringtie = true
                skip_bigwig = true
            }
        }

        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}', 'seqkit', 'seqkit/**'])
            // stable_path: All files in ${params.outdir}/ with stable content
            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
            assertAll(
                { assert workflow.success},
                { assert snapshot(
                    // Number of successful tasks
                    workflow.trace.succeeded().size(),
                    // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow").findAll { it.key != "SEQKIT_REPLACE" && it.key != "SEQKIT_REPLACE_U2T" },
                    // All stable path name, with a relative path
                    stable_name,
                    // All files with stable contents
                    stable_path
                ).match() }
            )
        }

        cleanup {
            // Only prune/delete on CI - keeping local VM state intact prevents
            // cross-test launchDir wipes that break nf-test snapshot walks.
            if (System.getenv("CI") == "true") {
                if (System.getenv("NFT_PROFILE")?.contains("docker")) {
                    "docker system prune -a -f --volumes".execute()
                }
                new File("${launchDir}").deleteDir()
            }
        }
    }

    test("Params: --remove_ribo_rna --ribo_removal_tool bowtie2 - stub") {

        options "-stub"

        when {
            params {
                outdir = "$outputDir"
                remove_ribo_rna = true
                ribo_removal_tool = 'bowtie2'
                // Skip processes already covered by default.nf.test (rRNA removal only affects read count, not BAM structure)
                skip_qc = true
                skip_stringtie = true
                skip_bigwig = true
            }
        }

        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}', 'seqkit', 'seqkit/**'])
            // stable_path: All files in ${params.outdir}/ with stable content
            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
            assertAll(
                { assert workflow.success},
                { assert snapshot(
                    // Number of successful tasks
                    workflow.trace.succeeded().size(),
                    // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow").findAll { it.key != "SEQKIT_REPLACE" && it.key != "SEQKIT_REPLACE_U2T" },
                    // All stable path name, with a relative path
                    stable_name,
                    // All files with stable contents
                    stable_path
                ).match() }
            )
        }

        cleanup {
            // Only prune/delete on CI - keeping local VM state intact prevents
            // cross-test launchDir wipes that break nf-test snapshot walks.
            if (System.getenv("CI") == "true") {
                if (System.getenv("NFT_PROFILE")?.contains("docker")) {
                    "docker system prune -a -f --volumes".execute()
                }
                new File("${launchDir}").deleteDir()
            }
        }
    }
    test("Params: --remove_ribo_rna --ribo_removal_tool bowtie2 --bowtie2_rrna_index") {

        when {
            params {
                outdir             = "$outputDir"
                remove_ribo_rna    = true
                ribo_removal_tool  = 'bowtie2'
                bowtie2_rrna_index = '' // Pending PR of test dataset on nf-core/test-datasets:rnaseq
                skip_qc        = true
                skip_stringtie = true
                skip_bigwig    = true
            }
        }

        then {
            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}', 'seqkit', 'seqkit/**'])
            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
            assertAll(
                { assert workflow.success},
                { assert snapshot(
                    // Number of tasks should be lower than the standard bowtie2 test because the index build step is skipped
                    workflow.trace.succeeded().size(),
                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow").findAll { it.key != "SEQKIT_REPLACE" && it.key != "SEQKIT_REPLACE_U2T" },
                    stable_name,
                    stable_path
                ).match() }
            )
        }

        cleanup {
            if (System.getenv("CI") == "true") {
                if (System.getenv("NFT_PROFILE")?.contains("docker")) {
                    "docker system prune -a -f --volumes".execute()
                }
                new File("${launchDir}").deleteDir()
            }
        }
    }
    test("Params: --remove_ribo_rna --ribo_removal_tool bowtie2 --bowtie2_rrna_index - stub") {

        options "-stub"

        when {
            params {
                outdir             = "$outputDir"
                remove_ribo_rna    = true
                ribo_removal_tool  = 'bowtie2'
                bowtie2_rrna_index = '' // Pending PR of test dataset on nf-core/test-datasets:rnaseq
                skip_qc        = true
                skip_stringtie = true
                skip_bigwig    = true
            }
        }

        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}', 'seqkit', 'seqkit/**'])
            // stable_path: All files in ${params.outdir}/ with stable content
            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
            assertAll(
                { assert workflow.success},
                { assert snapshot(
                    // Number of successful tasks
                    workflow.trace.succeeded().size(),
                    // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow").findAll { it.key != "SEQKIT_REPLACE" && it.key != "SEQKIT_REPLACE_U2T" },
                    // All stable path name, with a relative path
                    stable_name,
                    // All files with stable contents
                    stable_path
                ).match() }
            )
        }

        cleanup {
            // Only prune/delete on CI - keeping local VM state intact prevents
            // cross-test launchDir wipes that break nf-test snapshot walks.
            if (System.getenv("CI") == "true") {
                if (System.getenv("NFT_PROFILE")?.contains("docker")) {
                    "docker system prune -a -f --volumes".execute()
                }
                new File("${launchDir}").deleteDir()
            }
        }
    }
}