Merge pull request #1245 from adamrtalbot/nf-test_quantify_rsem

nf test quantify rsem
nf-core · Mar 8, 2024 · 417d0d1 · 417d0d1
2 parents 4823279 + 74853ce
commit 417d0d1
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diff --git a/subworkflows/local/quantify_rsem/tests/main.nf.test b/subworkflows/local/quantify_rsem/tests/main.nf.test
@@ -0,0 +1,71 @@
+nextflow_workflow {
+
+    name "Test Workflow QUANTIFY_RSEM"
+    script "../main.nf"
+    workflow "QUANTIFY_RSEM"
+    config "./nextflow.config"
+
+    tag 'RSEM_CALCULATEEXPRESSION'
+    tag 'RSEM_MERGE_COUNTS'
+    tag 'BAM_SORT_STATS_SAMTOOLS'
+
+    test("homo_sapiens") {
+
+        setup {
+            run("RSEM_PREPAREREFERENCE") {
+                script "../../../../modules/nf-core/rsem/preparereference/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true))
+                    input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true))
+                    """
+                }
+            }
+        }
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', strandedness: 'forward' ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = RSEM_PREPAREREFERENCE.out.index
+                input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.counts_gene,
+                    workflow.out.counts_transcript,
+                    workflow.out.stat,
+                    workflow.out.bam_star,
+                    workflow.out.bam_genome,
+                    workflow.out.bam_transcript,
+                    workflow.out.counts_transcript,
+                    workflow.out.bam,
+                    workflow.out.bai,
+                    workflow.out.csi,
+                    workflow.out.stats,
+                    workflow.out.flagstat,
+                    workflow.out.idxstats,
+                    workflow.out.merged_counts_gene,
+                    workflow.out.merged_tpm_gene,
+                    workflow.out.merged_counts_transcript,
+                    workflow.out.merged_tpm_transcript,
+                    workflow.out.versions
+                ).match()
+                },
+                { assert snapshot(file(workflow.out.logs[0][1]).name).match('logs') }
+            )
+        }
+    }
+
+}
diff --git a/subworkflows/local/quantify_rsem/tests/main.nf.test.snap b/subworkflows/local/quantify_rsem/tests/main.nf.test.snap
@@ -0,0 +1,110 @@
+{
+    "logs": {
+        "content": [
+            "test.log"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-07T18:25:31.476361"
+    },
+    "homo_sapiens": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    "test.genes.results:md5,c7ec226f76736ea805771e73553ae359"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    "test.isoforms.results:md5,99f7f80aa505b44ca429fdebbd7dd5d8"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    [
+                        "test.cnt:md5,76249e6b2f3c104f414aae596ba2c2f4",
+                        "test.model:md5,a7a4bc1734918ef5848604e3362b83e2",
+                        "test.theta:md5,de2e4490c98cc5383a86ae8225fd0a28"
+                    ]
+                ]
+            ],
+            [
+
+            ],
+            [
+
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    "test.transcript.bam:md5,ed681d39f5700ffc74d6321525330d93"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    "test.isoforms.results:md5,99f7f80aa505b44ca429fdebbd7dd5d8"
+                ]
+            ],
+            [
+
+            ],
+            [
+
+            ],
+            [
+
+            ],
+            [
+
+            ],
+            [
+
+            ],
+            [
+
+            ],
+            [
+                "rsem.merged.gene_counts.tsv:md5,f3b586000c97c89aec45360772e73df1"
+            ],
+            [
+                "rsem.merged.gene_tpm.tsv:md5,e6ae3dfa9913a7c15b705ec27c376212"
+            ],
+            [
+                "rsem.merged.transcript_counts.tsv:md5,235c002b811360183494a2aac74d1f5b"
+            ],
+            [
+                "rsem.merged.transcript_tpm.tsv:md5,d38f22667e3b8012f1d783b8d5159ccc"
+            ],
+            [
+                "versions.yml:md5,2aa5252eb2ffb409cf556a165d40f8a9",
+                "versions.yml:md5,ae1676b60b6335fff8f1188288103a1c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-07T18:15:03.001083"
+    }
+}
diff --git a/subworkflows/local/quantify_rsem/tests/nextflow.config b/subworkflows/local/quantify_rsem/tests/nextflow.config
@@ -0,0 +1,12 @@
+process {
+
+    // Needs the glob to force the config to be applied
+    withName: "RSEM_PREPAREREFERENCE" {
+        ext.args = "--star "
+    }
+
+    withName: "RSEM_CALCULATEEXPRESSION" {
+        ext.args = '--star --star-gzipped-read-file'
+    }
+
+}