update snaps

nf-core · Dec 19, 2024 · 970fded · 970fded
1 parent 6137d5f
commit 970fded
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Showing 4 changed files with 71 additions and 31 deletions.
diff --git a/subworkflows/local/fusioncatcher_workflow/tests/main.nf.test b/subworkflows/local/fusioncatcher_workflow/tests/main.nf.test
@@ -11,7 +11,7 @@ nextflow_workflow {
     // Test
     test("FUSIONCATCHER_WORKFLOW - Homo sapiens - FASTQs chr4") {
 
-        setup {
+        /*setup {
             // Download reference files for fusioncatch
             run("FUSIONCATCHER_DOWNLOAD") {
                 script "../../../../modules/local/fusioncatcher/download/main.nf"
@@ -21,8 +21,9 @@ nextflow_workflow {
                 """
                 }
             }
-        }
+        }*/
 
+        // TODO: get smaller reference files for fusioncatcher
         when {
             workflow {
                 """
@@ -37,7 +38,8 @@ nextflow_workflow {
                     ] )
 
                 // ch_references
-                input[1] = FUSIONCATCHER_DOWNLOAD.out.reference 
+                input[1] = Channel.fromPath("complete/with/your/local/path", checkIfExists: true)
+                    .map{ [[id: "human_v102" ], it] } //FUSIONCATCHER_DOWNLOAD.out.reference 
 
                 // fusioncatcher (boolean)
                 input[2] = true

diff --git a/subworkflows/local/fusioncatcher_workflow/tests/main.nf.test.snap b/subworkflows/local/fusioncatcher_workflow/tests/main.nf.test.snap
@@ -32,6 +32,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-12-18T21:26:47.477736"
+        "timestamp": "2024-12-19T17:44:38.284199"
     }
 }
diff --git a/tests/test_build.nf.test.snap b/tests/test_build.nf.test.snap
@@ -2,25 +2,16 @@
     "test_build": {
         "content": [
             [
-                "fastqc",
-                "fastqc/test_1_fastqc.html",
-                "fastqc/test_1_fastqc.zip",
-                "fastqc/test_2_fastqc.html",
-                "fastqc/test_2_fastqc.zip",
-                "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml"
+
             ],
             [
-                "test_1_fastqc.html:md5,fce82f01594d12b109776ced37ec0739",
-                "test_1_fastqc.zip:md5,fd0eae421abf76c38f60656bc0fcf5cf",
-                "test_2_fastqc.html:md5,40f5f42c62a0e36def4fc3d3c48089cd",
-                "test_2_fastqc.zip:md5,1aaf903d6ea3957abe6f03ad832f82fa"
+
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-12-18T21:05:30.032816"
+        "timestamp": "2024-12-19T12:50:27.263029"
     }
 }
diff --git a/tests/test_cosmic.nf.test.snap b/tests/test_cosmic.nf.test.snap
@@ -1,4 +1,51 @@
 {
+    "test cosmic no fastp trim build": {
+        "content": [
+            9,
+            null,
+            [
+                "bedops",
+                "bedops/Homo_sapiens.GRCh38.102_rrna_intervals.gtf.bed",
+                "gatk4",
+                "gatk4/Homo_sapiens.GRCh38.102.dna.primary_assembly.dict",
+                "gffread",
+                "gffread/Homo_sapiens.GRCh38.102.fasta",
+                "pipeline_info",
+                "references",
+                "references/ensembl",
+                "references/ensembl/Homo_sapiens.GRCh38.102.chr.gtf",
+                "references/ensembl/Homo_sapiens.GRCh38.102.dna.primary_assembly.fa",
+                "references/ensembl/Homo_sapiens.GRCh38.102.dna.primary_assembly.fa.fai",
+                "references/ensembl/Homo_sapiens.GRCh38.102.genepred",
+                "references/ensembl/Homo_sapiens.GRCh38.102.gtf",
+                "references/ensembl/Homo_sapiens.GRCh38.102.refflat",
+                "references/ensembl/Homo_sapiens.GRCh38.102_rrna_intervals.gtf.interval_list",
+                "references/hgnc",
+                "references/hgnc/HGNC-DB-timestamp.txt",
+                "references/hgnc/hgnc_complete_set.txt",
+                "rrnatranscripts",
+                "rrnatranscripts/Homo_sapiens.GRCh38.102_rrna_intervals.gtf"
+            ],
+            [
+                "Homo_sapiens.GRCh38.102_rrna_intervals.gtf.bed:md5,5bc3ccc76735ae46699a75269f0ea65b",
+                "Homo_sapiens.GRCh38.102.dna.primary_assembly.dict:md5,092f1bf29fce906ff7b5ece02b4b21c8",
+                "Homo_sapiens.GRCh38.102.fasta:md5,d1f17b045dc60c49f2cc29e30006afc0",
+                "Homo_sapiens.GRCh38.102.chr.gtf:md5,0069687307852c63596b4d2ebdbbaf0c",
+                "Homo_sapiens.GRCh38.102.dna.primary_assembly.fa.fai:md5,d527f3eb6b664020cf4d882b5820056f",
+                "Homo_sapiens.GRCh38.102.genepred:md5,59c577ca4ab033c0ce1feac1e387bcab",
+                "Homo_sapiens.GRCh38.102.gtf:md5,defac755cd9aa4e82ec33398c27745ef",
+                "Homo_sapiens.GRCh38.102.refflat:md5,ef095e13743811c31d44752c32e9673e",
+                "Homo_sapiens.GRCh38.102_rrna_intervals.gtf.interval_list:md5,0abf61877f65247b15c438d605d85599",
+                "hgnc_complete_set.txt:md5,a563a2f8432ec0ab7d3dc74d769102b8",
+                "Homo_sapiens.GRCh38.102_rrna_intervals.gtf:md5,744bf505deb50837b15441e808cad345"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-12-19T14:45:08.191019"
+    },
     "test cosmic no fastp trim": {
         "content": [
             1,
@@ -20,17 +67,17 @@
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml"
             ],
             [
-                "test_1_fastqc.html:md5,fce82f01594d12b109776ced37ec0739",
-                "test_1_fastqc.zip:md5,166d13bbf5ebfcb24eb30c78b129a172",
-                "test_2_fastqc.html:md5,40f5f42c62a0e36def4fc3d3c48089cd",
-                "test_2_fastqc.zip:md5,4747768318b29ce4effe6c572ccbc36c"
+                "test_1_fastqc.html:md5,413a6e28e6dd182616fb5859822e288e",
+                "test_1_fastqc.zip:md5,793d81ea4349817b15ff37f6b053f870",
+                "test_2_fastqc.html:md5,820795d75b698565195c6a20c492c9fb",
+                "test_2_fastqc.zip:md5,179dee147c92fed9b552a2f2f82b7367"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-12-18T21:06:31.911972"
+        "timestamp": "2024-12-19T12:51:54.89817"
     },
     "test cosmic with fastp trim": {
         "content": [
@@ -70,25 +117,25 @@
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml"
             ],
             [
-                "test.fastp.html:md5,d26a7f988fd5ed667832d391ab06e202",
+                "test.fastp.html:md5,4a1627af1a54b4f7b2dcf43c34369f04",
                 "test.fastp.json:md5,ebf549d5793aa40efcd9e1ca41504f26",
                 "test.fastp.log:md5,1c04b14e212aac5ace51f9bd25859f23",
                 "test_1.fastp.fastq.gz:md5,2a5519a03fb226ae2379b1150b02ff0b",
                 "test_2.fastp.fastq.gz:md5,4b8d3865b857e6bfae0035a45b2cdc27",
-                "test_1_fastqc.html:md5,fce82f01594d12b109776ced37ec0739",
-                "test_1_fastqc.zip:md5,f9e7e4dbf71703d98214cfd5cb79ee07",
-                "test_2_fastqc.html:md5,40f5f42c62a0e36def4fc3d3c48089cd",
-                "test_2_fastqc.zip:md5,7428e5d3c26f0934c75b15de29d6af5c",
-                "test_trimmed_1_fastqc.html:md5,2c2256226962e9be8c20e5720b8a51ab",
-                "test_trimmed_1_fastqc.zip:md5,3b8731204e07bfe7a6ecce66ba8617db",
-                "test_trimmed_2_fastqc.html:md5,343c493ba215089723e9d4df7180a0fc",
-                "test_trimmed_2_fastqc.zip:md5,fcec86b3067854ffdadd00db615f0cdd"
+                "test_1_fastqc.html:md5,413a6e28e6dd182616fb5859822e288e",
+                "test_1_fastqc.zip:md5,f4c865fd4ae054f2a98ae971ffdef576",
+                "test_2_fastqc.html:md5,820795d75b698565195c6a20c492c9fb",
+                "test_2_fastqc.zip:md5,67466d294966125f9e4e11333a231080",
+                "test_trimmed_1_fastqc.html:md5,6919dace995f86210c983eff554c43e7",
+                "test_trimmed_1_fastqc.zip:md5,069fd1c49854f8aea29acf5d870fa9cf",
+                "test_trimmed_2_fastqc.html:md5,6b567bc53367bb126896d7aa27e0c6f4",
+                "test_trimmed_2_fastqc.zip:md5,a65ef7a18c69fb6d8b3d0a2f9f87d938"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-12-18T21:06:00.758494"
+        "timestamp": "2024-12-19T12:51:19.311692"
     }
 }