Added parameter spades_use_contigs_not_scaffolds

nf-core · Jan 20, 2025 · b1eb9ed · b1eb9ed
1 parent 84e7186
commit b1eb9ed
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Showing 3 changed files with 10 additions and 4 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -59,6 +59,7 @@ params {
     // assembly options
     coassemble_group                     = false
     spades_options                       = null
+    spades_use_contigs_not_scaffolds     = false
     megahit_options                      = null
     skip_spades                          = false
     skip_spadeshybrid                    = false

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -570,6 +570,10 @@
                     "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\")"
                 },
+                "spades_use_contigs_not_scaffolds": {
+                    "type": "boolean",
+                    "description": "Specify whether to use contigs or scaffolds assembled by SPAdes"
+                },
                 "megahit_options": {
                     "type": "string",
                     "description": "Additional custom options for MEGAHIT.",

diff --git a/workflows/mag.nf b/workflows/mag.nf
@@ -380,10 +380,11 @@ workflow MAG {
 
         if (!params.single_end && !params.skip_spades) {
             METASPADES(ch_short_reads_spades.map { meta, reads -> [meta, reads, [], []] }, [], [])
-            ch_spades_assemblies = METASPADES.out.contigs.map { meta, assembly ->
-                def meta_new = meta + [assembler: 'SPAdes']
-                [meta_new, assembly]
-            }
+            ch_spades_assemblies = ( params.spades_use_contigs_not_scaffolds ? METASPADES.out.contigs : METASPADES.out.scaffolds )
+                .map { meta, assembly ->
+                    def meta_new = meta + [assembler: 'SPAdes']
+                    [meta_new, assembly]
+                }
             ch_assembled_contigs = ch_assembled_contigs.mix(ch_spades_assemblies)
             ch_versions = ch_versions.mix(METASPADES.out.versions.first())
         }