Merge pull request #705 from nf-core/always-meta-parameter-metaspades

Always run in METASPADES --meta mode
nf-core · Oct 25, 2024 · 76e056a · 76e056a
2 parents babacaa + 723e621
commit 76e056a
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -263,13 +263,13 @@ process {
     }
 
     withName: METASPADES {
-        ext.args   = params.spades_options ?: '--meta'
+        ext.args   = params.spades_options ? params.spades_options + ' --meta' : '--meta'
         ext.prefix = { "SPAdes-${meta.id}" }
         publishDir = [path: { "${params.outdir}/Assembly/SPAdes" }, mode: params.publish_dir_mode, pattern: "*.{fasta.gz,gfa.gz,fa.gz,log}"]
     }
 
     withName: METASPADESHYBRID {
-        ext.args   = params.spades_options ?: '--meta'
+        ext.args   = params.spades_options ? params.spades_options + ' --meta' : '--meta'
         ext.prefix = { "SPAdesHybrid-${meta.id}" }
         publishDir = [path: { "${params.outdir}/Assembly/SPAdesHybrid" }, mode: params.publish_dir_mode, pattern: "*.{fasta.gz,gfa.gz,fa.gz,log}"]
     }

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -551,8 +551,8 @@
                 },
                 "spades_options": {
                     "type": "string",
-                    "description": "Additional custom options for SPAdes and SPAdesHybrid. You must also specify `--meta` to run SPAdes in metagenomic mode if customising these options!",
-                    "help_text": "An example is adjusting k-mers (\"-k 21,33,55,77\") or adding [advanced options](https://github.com/ablab/spades#advanced-options). But not -t, -m, -o or --out-prefix, because these are already in use. Must be used like this: --spades_options \"-k 21,33,55,77\")"
+                    "description": "Additional custom options for SPAdes and SPAdesHybrid. Do not specify `--meta` as this will be added for you!",
+                    "help_text": "An example is adjusting k-mers (\"-k 21,33,55,77\") or adding [advanced options](https://github.com/ablab/spades#advanced-options). But not --meta, -t, -m, -o or --out-prefix, because these are already in use. Must be used like this: --spades_options \"-k 21,33,55,77\")"
                 },
                 "megahit_options": {
                     "type": "string",