Updated README and snapshot

Plant-Food-Research-Open · Dec 11, 2024 · ab3ae37 · ab3ae37
1 parent f980772
commit ab3ae37
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Showing 3 changed files with 21 additions and 4 deletions.
diff --git a/README.md b/README.md
@@ -39,11 +39,12 @@
   - Optionally, allow or remove iso-forms
   - Remove BRAKER models from Liftoff loci
   - Merge Liftoff and BRAKER models
-  - Optionally, remove models with ORFs shorter than `N` amino acids
   - Optionally, remove models without any EggNOG-mapper hits
 - [EggNOG-mapper](https://github.com/eggnogdb/eggnog-mapper): Add functional annotation to gff
 - [GenomeTools](https://github.com/genometools/genometools): GFF format validation
-- [GffRead](https://github.com/gpertea/gffread): Extraction of protein sequences
+- [GffRead](https://github.com/gpertea/gffread)
+  - Extraction of protein sequences
+  - Optionally, remove models with ORFs shorter than `N` amino acids
 - [OrthoFinder](https://github.com/davidemms/OrthoFinder): Perform phylogenetic orthology inference across genomes
 - [GffCompare](https://github.com/gpertea/gffcompare): Compare and benchmark against an existing annotation
 - [BUSCO](https://gitlab.com/ezlab/busco): Completeness statistics for genome and annotation through proteins

diff --git a/tests/minimal/main.nf.test b/tests/minimal/main.nf.test
@@ -38,6 +38,8 @@ nextflow_pipeline {
                 ['**']
             )
 
+            def summary_stats = (Map) new groovy.json.JsonSlurper().parseText(file("$outputDir/genepal_data/summary_stats.json").text)
+
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -46,6 +48,7 @@ nextflow_pipeline {
                         'versions': removeNextflowVersion("$outputDir/pipeline_info/genepal_software_mqc_versions.yml"),
                         'stable paths': stable_path,
                         'stable names': getRelativePath(stable_name, outputDir),
+                        'summary_stats': summary_stats
                     ]
                 ).match() }
             )

diff --git a/tests/minimal/main.nf.test.snap b/tests/minimal/main.nf.test.snap
@@ -90,13 +90,26 @@
                     "genepal_report.html",
                     "multiqc_report.html",
                     "pipeline_info"
-                ]
+                ],
+                "summary_stats": {
+                    "stats": [
+                        {
+                            "ID": "a_thaliana",
+                            "Genes": 252,
+                            "mRNA": 265,
+                            "CDS": 1340,
+                            "Exons": 1340,
+                            "Intron": 1075,
+                            "Non canon splice sites": 18
+                        }
+                    ]
+                }
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-12-11T21:49:09.751422"
+        "timestamp": "2024-12-12T09:36:52.952048"
     }
 }