Merge pull request #58 from nf-core/bug-fix-shcema-pattern

samplesheet schema pattern fix, and end-to-end snapshot updated

Author: vagkaratzas

assets/schema_input.json

@@ -17,8 +17,8 @@
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$",
-                "errorMessage": "Fasta file for each sample must be provided, cannot contain spaces and must have extension '.fa.gz', '.fa', '.fasta', or '.fasta.gz'"
+                "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.(fa|fasta|faa|fas)(\\.gz)?$",
+                "errorMessage": "Fasta file for each sample must be provided, cannot contain spaces and must have extension '.faa', '.fa', '.fas' or '.fasta', and optionally be compressed (.gz)"
             }
         },
         "required": ["id", "fasta"]

tests/default.nf.test

@@ -27,6 +27,8 @@ nextflow_pipeline {
             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_proteinannotator_software_mqc_versions.yml"),
                     // All stable path name, with a relative path

tests/default.nf.test.snap

@@ -13,7 +13,9 @@
             [
                 "multiqc",
                 "multiqc/multiqc_data",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
+                "multiqc/multiqc_data/multiqc.parquet",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
                 "multiqc/multiqc_data/multiqc_software_versions.txt",
@@ -26,19 +28,15 @@
                 "seqkit/T1026.tsv"
             ],
             [
-                "multiqc.log:md5,e53e3d119c66404ce20772bed762a05f",
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-                "multiqc_data.json:md5,24edddc3d41115fe71cc9a7d9092ca96",
-                "multiqc_software_versions.txt:md5,c5b754560c24cc8da0c1e92febf6f37f",
-                "multiqc_sources.txt:md5,d2a044df39ce3c6abe5cdc2d67473490",
                 "T1024.tsv:md5,c8a3fd71b27b9455aa837e1d50026971",
                 "T1026.tsv:md5,b028126e117cf0979b6f907cb20c6958"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.1"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-06-03T17:59:05.58411"
+        "timestamp": "2025-12-01T13:29:43.423448494"
     }
 }