Merge pull request #447 from nf-core/add-pyrodigal-param

Prevent Pyrodigal from adding stop codon indicators

Author: jasmezz

CHANGELOG.md

@@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#437](https://github.com/nf-core/funcscan/pull/437) Fixed file name error when supplying already preprocessed CARD database for ARG workflow. (by @jasmezz)
 - [#446](https://github.com/nf-core/funcscan/pull/446) Updated antiSMASH modules to fix apptainer execution. (by @jasmezz and @jfy133)
 - [#448](https://github.com/nf-core/funcscan/pull/448) Fixed taxonomy merge to work with output from GTDB/SILVA/KALAMARI. (by @darcy220606)
+- [#447](https://github.com/nf-core/funcscan/pull/447) Added `--annotation_pyrodigal_usespecialstopcharacter` parameter to improve AMPlify screening. (by @jasmezz)
 
 ### `Dependencies`
 

conf/modules.config

@@ -201,6 +201,7 @@ process {
             params.annotation_pyrodigal_singlemode ? "-p single" : "-p meta",
             params.annotation_pyrodigal_closed ? "-c" : "",
             params.annotation_pyrodigal_forcenonsd ? "-n" : "",
+            params.annotation_pyrodigal_usespecialstopcharacter ? '' : '--no-stop-codon',
             "-g ${params.annotation_pyrodigal_transtable}",
         ].join(' ').trim()
     }

nextflow.config

@@ -66,6 +66,7 @@ params {
     annotation_pyrodigal_closed                     = false
     annotation_pyrodigal_transtable                 = 11
     annotation_pyrodigal_forcenonsd                 = false
+    annotation_pyrodigal_usespecialstopcharacter    = false
 
     annotation_bakta_db                             = null
     annotation_bakta_db_downloadtype                = 'full'

nextflow_schema.json

@@ -518,6 +518,13 @@
                     "fa_icon": "fas fa-barcode",
                     "description": "Forces Pyrodigal to scan for motifs.",
                     "help_text": "Forces Pyrodigal to a full scan for motifs rather than activating the Shine-Dalgarno RBS finder, the default scanner for Pyrodigal to train for motifs.\n\nFor more information check the Pyrodigal [documentation](https://pyrodigal.readthedocs.io).\n\n> Modifies tool parameter(s):\n> - PYRODIGAL: `-n`"
+                },
+                "annotation_pyrodigal_usespecialstopcharacter": {
+                    "type": "boolean",
+                    "fa_icon": "fa fa-star-of-life",
+                    "description": "This forces Pyrodigal to append asterisks (`*`) as stop codon indicators. Do not use when running AMP workflow.",
+                    "help_text": "Some downstream tools like AMPlify cannot process sequences containing non-sequence characters like the stop codon indicator `*`. Thus, this flag is deactivated by default. Activate this flag to revert the behaviour and have Pyrodigal append `*` as stop codon indicator to annotated sequences.\n\nFor more information check the Pyrodigal [documentation](https://pyrodigal.readthedocs.io).\n\n> Modifies tool parameter(s):\n> - PYRODIGAL: `--no-stop-codon`",
+                    "default": false
                 }
             },
             "fa_icon": "fas fa-file-signature"

ro-crate-metadata.json

@@ -47,7 +47,7 @@
     "deeparg_tsv_ARG": {
         "content": [
             "sample_1.align.daa.tsv:md5,21822364379fe8f991d27cdb52a33d1d",
-            "sample_2.align.daa.tsv:md5,f448465df58785a87cdee53691a77bfe",
+            "sample_2.align.daa.tsv:md5,d59287f357de198639bdca5dbaede173",
             "sample_1.mapping.ARG:md5,0e049e99eab4c55666062df21707d5b9",
             "sample_2.mapping.ARG:md5,0e049e99eab4c55666062df21707d5b9"
         ],

tests/test.nf.test.snap

@@ -3,7 +3,7 @@
         "content": [
             "sample_1.align.daa.tsv:md5,0e71c37318bdc6cba792196d0455293d",
             "sample_2.align.daa.tsv:md5,1092ecd3cd6931653168b46c7afeb9e3",
-            "sample_3.align.daa.tsv:md5,b79070fe26acd1a10ae3aaf06b0d5901",
+            "sample_3.align.daa.tsv:md5,a9ed2f0651d75b318fde07a76b06d7b8",
             true,
             true,
             true
@@ -71,8 +71,8 @@
             "sample_1.potential.ARG.normalized.tsv:md5,d6732b4b9765bfa47e27ba673e24b6a4",
             "sample_2.ARG.normalized.tsv:md5,1a19b894a7315aaae5f799e4539e6619",
             "sample_2.potential.ARG.normalized.tsv:md5,b241e22f9116d8f518ba8526d52ac4dc",
-            "sample_3.ARG.normalized.tsv:md5,d40d387176649ce80827420fef6a0169",
-            "sample_3.potential.ARG.normalized.tsv:md5,f331efd21ea143c180a15ae56a5210d3"
+            "sample_3.ARG.normalized.tsv:md5,d7577c0066a31e173f9cb545820650bf",
+            "sample_3.potential.ARG.normalized.tsv:md5,6d0889215f0ad7f601502ca67c0ca89e"
         ],
         "meta": {
             "nf-test": "0.9.0",