ED add stub tests to subworkflows

CHANGELOG.md

@@ -57,6 +57,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Saltshaker for downstream processing of mitochondrial SV calls from MitoSAlt [#775](https://github.com/nf-core/raredisease/pull/775)
 - Env variable NXF_SINGULARITY_NEW_PID_NAMESPACE = false to accommodate hisat2 running with latest Nextflow and Singularity [#775](https://github.com/nf-core/raredisease/pull/775)
 - Parameter `exclude_alt` to filter alignments to alt/unplaced contigs after alignment using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). Note that enabling this will restrict variant calling to these chromosomes [#803](https://github.com/nf-core/raredisease/pull/803)
+- Stub test for all the remaning subworkflows that were lacking it: align_bwa_bwamem2_bwameme, align_MT, align (bwameme - wes), align_sentieon, call_repeat_expansions, prepare_references, qc_bam [#820](https://github.com/nf-core/raredisease/pull/820)
 - Parameters `save_all_mapped_as_cram` and `save_noalt_mapped_as_cram` to replace `save_mapped_as_cram`, allowing independent control over publishing unfiltered and alt-filtered alignment files as CRAM [#807](https://github.com/nf-core/raredisease/pull/807)
 - Parameter `run_vcfanno_db_sanity_check` to check vcfanno database files for zero records and remove the corresponding annotation blocks from the TOML config before running vcfanno [#821](https://github.com/nf-core/raredisease/pull/821)
 - Added `--skip_split_multiallelics` parameter to allow users to skip the `bcftools norm --multiallelics -both` step in SNV calling (DeepVariant and Sentieon), which can cause indel quality degradation in single-interval runs [#823](https://github.com/nf-core/raredisease/pull/823)

subworkflows/local/align/tests/main.nf.test

@@ -148,7 +148,7 @@ nextflow_workflow {
             )
         }
     }
-    test("align bwamem2 - wes") {
+    test("align bwamem2 - wes, stub") {
 
         options "-stub"
 
@@ -352,4 +352,105 @@ nextflow_workflow {
             )
         }
     }
+
+
+
+    test("align bwameme - wes, stub") {
+
+        options "-stub"
+
+        setup {
+            run("BWAMEME_INDEX", alias: 'GENOME_MEME') {
+                script "modules/nf-core/bwameme/index/main.nf"
+                process {
+                    """
+                    input[0] = channel.of([
+                        [id:'genome'],
+                        file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta', checkIfExists: true)
+                    ])
+                    """
+                }
+            }
+        }
+
+
+        when {
+            params {
+                pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/'
+                platform            = "illumina"
+                min_trimmed_length  = 50
+                mito_name           = "MT"
+                outdir              = "$outputDir"
+            }
+            workflow {
+                """
+                input[0]  = channel.empty()
+                input[1]  = channel.empty()
+                input[2]  = channel.empty()
+                input[3]  = GENOME_MEME.out.index.collect()
+                input[4]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect()
+                input[5]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect()
+                input[6]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect()
+                input[7] = channel.fromList([
+                    [[ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky'  ], // meta map
+                    [
+                        file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true),
+                        file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true)
+                    ]],
+                    [[ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky'  ], // meta map
+                    [
+                        file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz', checkIfExists: true),
+                        file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz', checkIfExists: true)
+                    ]],
+                    [[ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'",  'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky'  ], // meta map
+                    [
+                        file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz', checkIfExists: true),
+                        file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true)
+                    ]]
+                ])
+                input[8]  = channel.empty()
+                input[9]  = MT_MEM2.out.index.collect()
+                input[10] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect()
+                input[11] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect()
+                input[12] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect()
+                input[13] = channel.empty()
+                input[14] = SHIFTMT_MEM2.out.index.collect()
+                input[15] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect()
+                input[16] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect()
+                input[17] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect()
+                input[18] = true
+                input[19] = "bwameme"
+                input[20] = "wgs"
+                input[21] = false
+                input[22] = false
+                input[23] = 3072
+                input[24] = "bwamem2"
+                input[25] = "illumina"
+                input[26] = false
+                input[27] = 4
+                input[28] = true
+                input[29] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                        workflow.out.publish.flatten()
+                            .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) }
+                            .collect { new File(it).name }
+                            .sort(),
+                        workflow.out.genome_marked_bam_bai
+                            .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] },
+                        workflow.out.mt_bam_bai
+                            .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] },
+                        workflow.out.mtshift_bam_bai
+                            .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }
+                    ).match()
+                }
+            )
+        }
+    }
 }