Added 1 to filter_genes_by_aa_length to exclude stop codon from filte…

…r length
Plant-Food-Research-Open · Dec 15, 2024 · c65ebaa · c65ebaa
1 parent ab3ae37
commit c65ebaa
Show file tree

Hide file tree

Showing 4 changed files with 10 additions and 10 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v0.6.0 - [10-Dec-2024]
+## v0.6.0 - [16-Dec-2024]
 
 ### 'Added'
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -241,7 +241,7 @@ process { // SUBWORKFLOW: GFF_MERGE_CLEANUP
     }
 
     withName: '.*:GFF_MERGE_CLEANUP:FILTER_BY_ORF_SIZE' {
-        ext.args = params.filter_genes_by_aa_length ? "--no-pseudo --keep-genes -C -l ${params.filter_genes_by_aa_length * 3}" : ''
+        ext.args = params.filter_genes_by_aa_length ? "--no-pseudo --keep-genes -C -l ${ ( params.filter_genes_by_aa_length + 1 ) * 3 }" : ''
     }
 
     withName: '.*:GFF_MERGE_CLEANUP:GT_GFF3' {

diff --git a/docs/parameters.md b/docs/parameters.md
@@ -59,13 +59,13 @@ A Nextflow pipeline for consensus, phased and pan-genome annotation.
 
 ## Post-annotation filtering options
 
-| Parameter                     | Description                                                                                                                            | Type      | Default | Required | Hidden |
-| ----------------------------- | -------------------------------------------------------------------------------------------------------------------------------------- | --------- | ------- | -------- | ------ |
-| `allow_isoforms`              | Allow multiple isoforms for gene models                                                                                                | `boolean` | True    |          |        |
-| `enforce_full_intron_support` | Require every model to have external evidence for all its introns                                                                      | `boolean` | True    |          |        |
-| `filter_liftoff_by_hints`     | Use BRAKER hints to filter Liftoff models                                                                                              | `boolean` | True    |          |        |
-| `eggnogmapper_purge_nohits`   | Purge transcripts which do not have a hit against eggnog                                                                               | `boolean` |         |          |        |
-| `filter_genes_by_aa_length`   | Filter genes with open reading frames shorter than the specified number of amino acids. If set to `null`, this filter step is skipped. | `integer` | 24      |          |        |
+| Parameter                     | Description                                                                                                                                                     | Type      | Default | Required | Hidden |
+| ----------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------- | ------- | -------- | ------ |
+| `allow_isoforms`              | Allow multiple isoforms for gene models                                                                                                                         | `boolean` | True    |          |        |
+| `enforce_full_intron_support` | Require every model to have external evidence for all its introns                                                                                               | `boolean` | True    |          |        |
+| `filter_liftoff_by_hints`     | Use BRAKER hints to filter Liftoff models                                                                                                                       | `boolean` | True    |          |        |
+| `eggnogmapper_purge_nohits`   | Purge transcripts which do not have a hit against eggnog                                                                                                        | `boolean` |         |          |        |
+| `filter_genes_by_aa_length`   | Filter genes with open reading frames shorter than the specified number of amino acids excluding the stop codon. If set to `null`, this filter step is skipped. | `integer` | 24      |          |        |
 
 ## Annotation output options
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -277,7 +277,7 @@
                     "type": "integer",
                     "default": 24,
                     "fa_icon": "fas fa-hashtag",
-                    "description": "Filter genes with open reading frames shorter than the specified number of amino acids. If set to `null`, this filter step is skipped.",
+                    "description": "Filter genes with open reading frames shorter than the specified number of amino acids excluding the stop codon. If set to `null`, this filter step is skipped.",
                     "minimum": 3
                 }
             }