Merge pull request #43 from nf-core/refactor-config

Refactor config

conf/modules.config

@@ -12,12 +12,6 @@
 
 process {
 
-    publishDir = [
-        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-    ]
-
     withName: SAMPLESHEET_CHECK {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },
@@ -34,20 +28,12 @@ process {
         ]
     }
 
-    withName: UNTAR {
-        publishDir = [
-            path: { "${params.outdir}/databases" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
     withName: FASTQC {
         ext.args = '--quiet'
         ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
         publishDir = [
             path: { "${params.outdir}/fastqc/raw" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
             pattern: '*.html'
         ]
     }
@@ -57,7 +43,7 @@ process {
         ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
         publishDir = [
             path: { "${params.outdir}/fastqc/processed" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
             pattern: '*.html'
         ]
     }
@@ -73,8 +59,9 @@ process {
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
             path: { "${params.outdir}/fastp" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
-            pattern: '*.fastq.gz'
+            pattern: '*.fastq.gz',
+            enabled: params.save_preprocessed_reads
         ]
     }
 
@@ -92,8 +79,9 @@ process {
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
             path: { "${params.outdir}/fastp" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
-            pattern: '*.fastq.gz'
+            pattern: '*.fastq.gz',
+            enabled: params.save_preprocessed_reads
         ]
     }
 
@@ -108,8 +96,9 @@ process {
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
             path: { "${params.outdir}/adapterremoval" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
-            pattern: '*.fastq.gz'
+            pattern: '*.fastq.gz',
+            enabled: params.save_preprocessed_reads
         ]
     }
 
@@ -127,8 +116,9 @@ process {
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
             path: { "${params.outdir}/adapterremoval" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
-            pattern: '*.fastq.gz'
+            pattern: '*.fastq.gz',
+            enabled: params.save_preprocessed_reads
         ]
     }
 
@@ -136,8 +126,9 @@ process {
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
             path: { "${params.outdir}/porechop" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
-            pattern: '*.fastq.gz'
+            pattern: '*.fastq.gz',
+            enabled: params.save_preprocessed_reads
         ]
     }
 
@@ -151,7 +142,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/bbduk/" },
             mode: params.publish_dir_mode,
-            pattern: '*.{fastq.gz,log}'
+            pattern: '*.{fastq.gz,log}',
+            enabled: params.save_complexityfiltered_reads
         ]
     }
 
@@ -164,7 +156,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/prinseqplusplus/" },
             mode: params.publish_dir_mode,
-            pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz,log}'
+            pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz,log}',
+            enabled: params.save_complexityfiltered_reads
         ]
     }
 
@@ -173,7 +166,7 @@ process {
         ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/malt/${meta.db_name}" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
             pattern: '*.{rma6,tab,text,sam,log}'
         ]
     }
@@ -183,7 +176,7 @@ process {
         ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/kraken2/${meta.db_name}" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
             pattern: '*.{fastq.gz,txt}'
         ]
     }

nextflow.config

@@ -64,6 +64,7 @@ params {
     shortread_clipmerge_adapter2            = null
     shortread_clipmerge_minlength           = 15
     longread_clip                           = false
+    save_preprocessed_reads                 = false
 
     // Complexity filtering
     shortread_complexityfilter                           = false
@@ -73,6 +74,7 @@ params {
     shortread_complexityfilter_bbduk_mask                = false
     shortread_complexityfilter_prinseqplusplus_mode      = 'entropy'
     shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
+    save_complexityfiltered_reads                        = false
 
 
     // MALT

nextflow_schema.json

@@ -308,6 +308,10 @@
             "type": "integer",
             "default": 15
         },
+        "save_preprocessed_reads": {
+            "type": "boolean",
+            "default": false
+        },
         "shortread_complexityfilter_tool": {
             "type": "string",
             "default": "bbduk"
@@ -334,6 +338,10 @@
         "shortread_complexityfilter_prinseqplusplus_dustscore": {
             "type": "number",
             "default": 0.5
+        },
+        "save_complexityfiltered_reads": {
+            "type": "boolean",
+            "default": false
         }
     }
 }