More unused output removed and made them optional

conf/modules.config

@@ -41,7 +41,7 @@ process {
         ]
     }
 
-    withName: FIRST_CAT {
+    withName: 'FIRST_CAT' {
         publishDir = [
             enabled: false
         ]
@@ -51,7 +51,20 @@ process {
         publishDir = [
             path: { "${params.outdir}/concatenate" },
             mode: 'copy',
-            pattern: '*.gz'
+            pattern: '*.gz',
+            enabled: params.save_genomes_cat
+        ]
+    }
+
+    withName: GENOMEINDEX {
+        publishDir = [
+            enabled: params.save_genomes_cat
+        ]
+    }
+
+    withName: GINDEX_CAT {
+        publishDir = [
+            enabled: params.save_genomes_cat
         ]
     }
 
@@ -71,14 +84,41 @@ process {
 
     withName: 'SAMPLES_SKETCH' {
         ext.args = "rna --param-string k=${params.ksize}"
+        publishDir = [
+            enabled: params.save_sourmash
+        ]
     }
 
     withName: 'GENOMES_SKETCH' {
         ext.args = "rna --param-string k=${params.ksize}"
+        publishDir = [
+            enabled: params.save_sourmash
+        ]
     }
 
     withName: 'SOURMASH_GATHER' {
         ext.args = '--threshold-bp "50"'
+        publishDir = [
+            enabled: params.save_sourmash
+        ]
+    }
+
+    withName: 'SOURMASH_INDEX' {
+        publishDir = [
+            enabled: params.save_sourmash
+        ]
+    }
+
+    withName: 'GUNZIP_GFFS' {
+        publishDir = [
+            enabled: false
+        ]
+    }
+
+    withName: 'GUNZIP' {
+        publishDir = [
+            enabled: false
+        ]
     }
 
     withName: 'GINDEX_CAT' {
@@ -119,6 +159,17 @@ process {
 
     withName: SAMTOOLS_SORT {
         ext.prefix = { "${meta.id}.sorted" }
+        publishDir = [
+            pattern: "*.bam",
+            enabled: false
+        ]
+    }
+
+    withName: SAMTOOLS_INDEX {
+        publishDir = [
+            pattern: "*.bai",
+            enabled: false
+        ]
     }
 
     withName: '.*:FEATURECOUNTS' {

nextflow.config

@@ -34,6 +34,7 @@ params {
     // sourmash
     sourmash                    = false
     ksize                       = 21
+    save_sourmash               = false
 
     // BBmap options
     bbmap_minid                 = 0.9
@@ -49,6 +50,7 @@ params {
     multiqc_methods_description = null
 
     // Boilerplate options
+    save_genomes_cat             = false
     outdir                       = null
     publish_dir_mode             = 'copy'
     email                        = null

nextflow_schema.json

@@ -143,6 +143,11 @@
                 "save_bbmap_index": {
                     "type": "boolean",
                     "description": "Save ref folder containing the reference index"
+                },
+                "save_genomes_cat": {
+                    "type": "boolean",
+                    "description": "Save genomes concatenated file",
+                    "default": false
                 }
             }
         },
@@ -160,6 +165,11 @@
                     "type": "integer",
                     "default": 21,
                     "description": "K-mer size used by Sourmash"
+                },
+                "save_sourmash": {
+                    "type": "boolean",
+                    "description": "Save Sourmash outuput",
+                    "default": false
                 }
             }
         },

subworkflows/local/sourmash.nf

@@ -56,6 +56,7 @@ workflow SOURMASH {
             .set { ch_genome_sigs }
 
         GENOMES_INDEX(ch_genome_sigs, ksize)
+        ch_versions = ch_versions.mix(GENOMES_INDEX.out.versions)
 
         GENOMES_INDEX.out.signature_index
             .map{ meta, sig -> sig }