Run nf-test successfully in minimal and stub

Plant-Food-Research-Open · Dec 5, 2024 · e05a469 · e05a469
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diff --git a/.nf-core.yml b/.nf-core.yml
@@ -30,5 +30,5 @@ template:
   outdir: .
   skip_features:
     - igenomes
-  version: 0.5.0
+  version: 0.6.0
 update: null
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -25,7 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 10. Added an HTML report [#44](https://github.com/Plant-Food-Research-Open/genepal/issues/44)
 11. Added content type as text/html for the MultiQC and genepal reports
 12. Added sra-tools for RNASeq data download [#102](https://github.com/Plant-Food-Research-Open/genepal/issues/102)
-    
+
 ### `Fixed`
 
 1. Now using `${meta.id}_trim` as prefix for `FASTQC` files

diff --git a/CITATION.cff b/CITATION.cff
@@ -31,7 +31,7 @@ authors:
   - family-names: "Thomson"
     given-names: "Susan"
 title: "genepal: A Nextflow pipeline for genome and pan-genome annotation"
-version: 0.5.0
+version: 0.6.0
 date-released: 2024-11-21
 url: "https://github.com/Plant-Food-Research-Open/genepal"
 doi: 10.5281/zenodo.14195006
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
   This report has been generated by the <a href="https://github.com/plant-food-research-open/genepal" target="_blank">plant-food-research-open/genepal</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://github.com/plant-food-research-open/genepal/blob/0.5.0/docs/usage.md" target="_blank">documentation</a>.
+  <a href="https://github.com/plant-food-research-open/genepal/blob/0.6.0/docs/usage.md" target="_blank">documentation</a>.
 
 report_section_order:
   "plant-food-research-open-genepal-methods-description":

diff --git a/conf/modules.config b/conf/modules.config
@@ -286,7 +286,7 @@ process { // SUBWORKFLOW: GFF_STORE
     }
 
     withName: '.*:GFF_STORE:EXTRACT_PROTEINS' {
-        ext.args = params.add_attrs_to_gffread_fastas ? '-F -D -y' : '-y'
+        ext.args = params.add_attrs_to_proteins_cds_fastas ? '-F -D -y' : '-y'
         ext.prefix = { "${meta.id}.pep" }
 
         publishDir = [

diff --git a/docs/parameters.md b/docs/parameters.md
@@ -4,17 +4,19 @@ A Nextflow pipeline for consensus, phased and pan-genome annotation.
 
 ## Input/output options
 
-| Parameter                 | Description                                                                                              | Type      | Default | Required | Hidden |
-| ------------------------- | -------------------------------------------------------------------------------------------------------- | --------- | ------- | -------- | ------ |
-| `input`                   | Target assemblies listed in a CSV sheet                                                                  | `string`  |         | True     |        |
-| `protein_evidence`        | Protein evidence provided as a fasta file or multiple fasta files listed in a plain txt file             | `string`  |         | True     |        |
-| `eggnogmapper_db_dir`     | Eggnogmapper database directory                                                                          | `string`  |         |          |        |
-| `eggnogmapper_tax_scope`  | Eggnogmapper taxonomy scopre. Eukaryota: 2759, Viridiplantae: 33090, Archaea: 2157, Bacteria: 2, root: 1 | `integer` | 1       |          |        |
-| `rna_evidence`            | FASTQ/BAM samples listed in a CSV sheet                                                                  | `string`  |         |          |        |
-| `liftoff_annotations`     | Reference annotations listed in a CSV sheet                                                              | `string`  |         |          |        |
-| `orthofinder_annotations` | Additional annotations for orthology listed in a CSV sheet                                               | `string`  |         |          |        |
-| `outdir`                  | The output directory where the results will be saved                                                     | `string`  |         | True     |        |
-| `email`                   | Email address for completion summary.                                                                    | `string`  |         |          | True   |
+| Parameter                | Description                                                                                              | Type      | Default | Required | Hidden |
+| ------------------------ | -------------------------------------------------------------------------------------------------------- | --------- | ------- | -------- | ------ |
+| `input`                  | Target assemblies listed in a CSV sheet                                                                  | `string`  |         | True     |        |
+| `protein_evidence`       | Protein evidence provided as a fasta file or multiple fasta files listed in a plain txt file             | `string`  |         | True     |        |
+| `eggnogmapper_db_dir`    | Eggnogmapper database directory                                                                          | `string`  |         |          |        |
+| `eggnogmapper_tax_scope` | Eggnogmapper taxonomy scopre. Eukaryota: 2759, Viridiplantae: 33090, Archaea: 2157, Bacteria: 2, root: 1 | `integer` | 1       |          |
+
+|
+| `rna_evidence` | FASTQ/BAM samples listed in a CSV sheet | `string` | | | |
+| `liftoff_annotations` | Reference annotations listed in a CSV sheet | `string` | | | |
+| `orthofinder_annotations` | Additional annotations for orthology listed in a CSV sheet | `string` | | | |
+| `outdir` | The output directory where the results will be saved | `string` | | True | |
+| `email` | Email address for completion summary. | `string` | | | True |
 
 ## Repeat annotation options
 
@@ -68,10 +70,9 @@ A Nextflow pipeline for consensus, phased and pan-genome annotation.
 
 ## Annotation output options
 
-| Parameter                     | Description                          | Type      | Default | Required | Hidden |
-| ----------------------------- | ------------------------------------ | --------- | ------- | -------- | ------ |
-| `braker_save_outputs`         | Save BRAKER files                    | `boolean` |         |          |        |
-| `add_attrs_to_proteins_fasta` | Add gff attributes to proteins fasta | `boolean` |         |          |        |
+| Parameter             | Description       | Type      | Default | Required | Hidden |
+| --------------------- | ----------------- | --------- | ------- | -------- | ------ |
+| `braker_save_outputs` | Save BRAKER files | `boolean` |         |          |        |
 
 ## Evaluation options
 
@@ -104,3 +105,9 @@ Less common options for the pipeline, typically set in a config file.
 | `max_multiqc_email_size` | File size limit when attaching MultiQC reports to summary emails. | `string`  | 25.MB   |          | True   |
 | `monochrome_logs`        | Do not use coloured log outputs.                                  | `boolean` |         |          | True   |
 | `hook_url`               | Incoming hook URL for messaging service                           | `string`  |         |          | True   |
+
+## Other parameters
+
+| Parameter                     | Description | Type      | Default | Required | Hidden |
+| ----------------------------- | ----------- | --------- | ------- | -------- | ------ |
+| `add_attrs_to_gffread_fastas` |             | `boolean` |         |          |        |
diff --git a/nextflow.config b/nextflow.config
@@ -57,7 +57,7 @@ params {
 
     // Annotation output options
     braker_save_outputs                 = false
-    add_attrs_to_gffread_fastas         = false
+    add_attrs_to_proteins_cds_fastas         = false
 
     // Evaluation options
     busco_skip                          = false
@@ -261,7 +261,7 @@ manifest {
     description     = """A Nextflow pipeline for consensus, phased and pan-genome annotation."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
-    version         = '0.5.0'
+    version         = '0.6.0'
     doi             = 'https://doi.org/10.5281/zenodo.14195006'
 }
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -286,11 +286,6 @@
                     "type": "boolean",
                     "description": "Save BRAKER files",
                     "fa_icon": "fas fa-question-circle"
-                },
-                "add_attrs_to_proteins_fasta": {
-                    "type": "boolean",
-                    "fa_icon": "fas fa-question-circle",
-                    "description": "Add gff attributes to proteins fasta"
                 }
             }
         },
@@ -438,5 +433,10 @@
         {
             "$ref": "#/$defs/generic_options"
         }
-    ]
+    ],
+    "properties": {
+        "add_attrs_to_proteins_cds_fastas": {
+            "type": "boolean"
+        }
+    }
 }
diff --git a/tests/minimal/main.nf.test.snap b/tests/minimal/main.nf.test.snap
@@ -2,7 +2,7 @@
     "profile - test": {
         "content": [
             {
-                "successful tasks": 18,
+                "successful tasks": 20,
                 "versions": {
                     "AGAT_CONVERTSPGFF2GTF": {
                         "agat": "v1.4.0"
@@ -25,6 +25,12 @@
                     "CAT_PROTEIN_FASTAS": {
                         "pigz": "2.3.4"
                     },
+                    "EXTRACT_CDNA": {
+                        "gffread": "0.12.7"
+                    },
+                    "EXTRACT_CDS": {
+                        "gffread": "0.12.7"
+                    },
                     "EXTRACT_PROTEINS": {
                         "gffread": "0.12.7"
                     },
@@ -55,10 +61,12 @@
                         "tsebra": "1.1.2.5"
                     },
                     "Workflow": {
-                        "plant-food-research-open/genepal": "v0.5.0"
+                        "plant-food-research-open/genepal": "v0.6.0"
                     }
                 },
                 "stable paths": [
+                    "a_thaliana.cdna.fasta:md5,12b9bef973e488640aec8c04ba3882fe",
+                    "a_thaliana.cds.fasta:md5,b81060419355a590560f92aec8536281",
                     "a_thaliana.gt.gff3:md5,8ab16549095f605ff8715ac4a3de58ed",
                     "a_thaliana.pep.fasta:md5,4994c0393ca0245a1c57966d846d101e",
                     "a_thaliana.gff3:md5,d23d16cd86499d48a30ffb981ed27891",
@@ -67,6 +75,8 @@
                 "stable names": [
                     "annotations",
                     "annotations/a_thaliana",
+                    "annotations/a_thaliana/a_thaliana.cdna.fasta",
+                    "annotations/a_thaliana/a_thaliana.cds.fasta",
                     "annotations/a_thaliana/a_thaliana.gt.gff3",
                     "annotations/a_thaliana/a_thaliana.pep.fasta",
                     "etc",
@@ -81,9 +91,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-11-19T11:35:02.477202"
+        "timestamp": "2024-12-05T07:51:43.818374"
     }
-}
+}
diff --git a/tests/stub/main.nf.test.snap b/tests/stub/main.nf.test.snap
@@ -2,7 +2,7 @@
     "full - stub": {
         "content": [
             {
-                "successful tasks": 154,
+                "successful tasks": 162,
                 "versions": {
                     "AGAT_CONVERTSPGFF2GTF": {
                         "agat": "v1.4.0"
@@ -55,6 +55,12 @@
                     "EGGNOGMAPPER": {
                         "eggnog-mapper": "2.1.12"
                     },
+                    "EXTRACT_CDNA": {
+                        "gffread": "0.12.7"
+                    },
+                    "EXTRACT_CDS": {
+                        "gffread": "0.12.7"
+                    },
                     "EXTRACT_PROTEINS": {
                         "gffread": "0.12.7"
                     },
@@ -143,25 +149,33 @@
                         "tsebra": "1.1.2.5"
                     },
                     "Workflow": {
-                        "plant-food-research-open/genepal": "v0.5.0"
+                        "plant-food-research-open/genepal": "v0.6.0"
                     }
                 },
                 "stable paths": [
+                    "donghong.cdna.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
+                    "donghong.cds.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
                     "donghong.emapper.annotations:md5,d41d8cd98f00b204e9800998ecf8427e",
                     "donghong.emapper.hits:md5,d41d8cd98f00b204e9800998ecf8427e",
                     "donghong.emapper.seed_orthologs:md5,d41d8cd98f00b204e9800998ecf8427e",
                     "donghong.gt.gff3:md5,d41d8cd98f00b204e9800998ecf8427e",
                     "donghong.pep.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
+                    "red5_v2p1.cdna.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
+                    "red5_v2p1.cds.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
                     "red5_v2p1.emapper.annotations:md5,d41d8cd98f00b204e9800998ecf8427e",
                     "red5_v2p1.emapper.hits:md5,d41d8cd98f00b204e9800998ecf8427e",
                     "red5_v2p1.emapper.seed_orthologs:md5,d41d8cd98f00b204e9800998ecf8427e",
                     "red5_v2p1.gt.gff3:md5,d41d8cd98f00b204e9800998ecf8427e",
                     "red5_v2p1.pep.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
+                    "red5_v3.cdna.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
+                    "red5_v3.cds.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
                     "red5_v3.emapper.annotations:md5,d41d8cd98f00b204e9800998ecf8427e",
                     "red5_v3.emapper.hits:md5,d41d8cd98f00b204e9800998ecf8427e",
                     "red5_v3.emapper.seed_orthologs:md5,d41d8cd98f00b204e9800998ecf8427e",
                     "red5_v3.gt.gff3:md5,d41d8cd98f00b204e9800998ecf8427e",
                     "red5_v3.pep.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
+                    "red7_v5.cdna.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
+                    "red7_v5.cds.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
                     "red7_v5.emapper.annotations:md5,d41d8cd98f00b204e9800998ecf8427e",
                     "red7_v5.emapper.hits:md5,d41d8cd98f00b204e9800998ecf8427e",
                     "red7_v5.emapper.seed_orthologs:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -188,9 +202,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-11-21T12:34:14.056074"
+        "timestamp": "2024-12-05T07:56:38.915238"
     }
-}
+}