Remove params which shouldn't be changed by users anyway

nf-core · Feb 11, 2025 · f68d316 · f68d316
1 parent d4c6ce6
commit f68d316
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Showing 3 changed files with 3 additions and 17 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -137,10 +137,10 @@ process {
         ext.args   = [
             "--applications ${params.protein_annotation_interproscan_applications}",
             params.protein_annotation_interproscan_enableprecalc ? '' : '--disable-precalc',
-            params.protein_annotation_interproscan_enableresidueannot ? '' : '--disable-residue-annot',
-            params.protein_annotation_interproscan_disableresidueannottsv ? '' : '--enable-tsv-residue-annot',
+            '--disable-residue-annot',
+            '--enable-tsv-residue-annot',
             "--formats tsv"
-        ].join(' ').trim()
+        ].join(' ').trim() // Warning: Do not disable the flags "--enable-tsv-residue-annot" and "--formats tsv"! This would cause a run failure because the format of the resulting files would no longer be adequate for parsing by AMPcombi2.
     }
 
     withName: PROKKA {

diff --git a/nextflow.config b/nextflow.config
@@ -111,8 +111,6 @@ params {
     protein_annotation_interproscan_db_url                  = 'https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.72-103.0/interproscan-5.72-103.0-64-bit.tar.gz'
     protein_annotation_interproscan_applications            = 'PANTHER,ProSiteProfiles,ProSitePatterns,Pfam'
     protein_annotation_interproscan_enableprecalc           = false
-    protein_annotation_interproscan_enableresidueannot      = false
-    protein_annotation_interproscan_disableresidueannottsv  = false
 
     // Database downloading options
     save_db                                                 = false

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -572,18 +572,6 @@
                     "help_text": "This increases the speed of functional annotation with InterProScan by pre-calculating matches found in the UniProtKB, thereby identifying unique matches in the query sequences for faster annotation. By default this is turned off.\n\nFor more information about this flag see the tool [documentation](https://interproscan-docs.readthedocs.io/en/latest/HowToRun.html).\n\n> Modifies tool parameter(s):\n> - InterProScan: `---diasable-precalc`",
                     "description": "Pre-calculates residue mutual matches.",
                     "fa_icon": "fas fa-clock"
-                },
-                "protein_annotation_interproscan_enableresidueannot": {
-                    "type": "boolean",
-                    "help_text": "By default, this flag removes the residue annotation from the final XML and JSON output files, which we do not supply as output files from InterProScan.\n\nFor more information about this flag see the tool [documentation](https://interproscan-docs.readthedocs.io/en/latest/HowToRun.html).\n\n> Modifies tool parameter(s):\n> - InterProScan: `--disable-residue-annot`",
-                    "description": "Enable residue annotation in XML and JSON files.",
-                    "fa_icon": "fas fa-eraser"
-                },
-                "protein_annotation_interproscan_disableresidueannottsv": {
-                    "type": "boolean",
-                    "help_text": "This disables the addition of the annotations assigned according to the databases activated to the final `<sample>_interproscan.tsv` file.  Turning this on will remove the annotations from the final table. It is not recommended to use this option, as it will cause a run failure because the format of the resulting files will no longer be adequate for integration in the final summary tables. Currently, only applicable for AMPcombi2. \n\nFor more information about this flag see the tool [documentation](https://interproscan-docs.readthedocs.io/en/latest/HowToRun.html).\n\n> Modifies tool parameter(s):\n> - InterProScan: `--enable-tsv-residue-annot`\n",
-                    "description": "Removes annotations from TSV file.",
-                    "fa_icon": "fas fa-eraser"
                 }
             },
             "help_text": "This subworkflow adds additional protein annotations to all annotated coding regions. Currently, only annotation with InterProScan is integrated in the subworkflow.",