From 7ab3aa546b8e1d0388981757d259284bf67f5fc8 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Wed, 6 Apr 2022 10:27:11 +0200
Subject: [PATCH] refactor: use flags to publish reads

---
 conf/modules.config  | 25 ++++++++++++++-----------
 nextflow.config      |  2 ++
 nextflow_schema.json |  8 ++++++++
 3 files changed, 24 insertions(+), 11 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index f9cfe3b..b59850f 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -28,10 +28,6 @@ process {
         ]
     }
 
-    withName: UNTAR {
-        publishDir = [enabled: false]
-    }
-
     withName: FASTQC {
         ext.args = '--quiet'
         ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
@@ -64,7 +60,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/fastp" },
             mode: params.publish_dir_mode,
-            pattern: '*.fastq.gz'
+            pattern: '*.fastq.gz',
+            enabled: params.save_preprocessed_reads
         ]
     }
 
@@ -83,7 +80,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/fastp" },
             mode: params.publish_dir_mode,
-            pattern: '*.fastq.gz'
+            pattern: '*.fastq.gz',
+            enabled: params.save_preprocessed_reads
         ]
     }
 
@@ -99,7 +97,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/adapterremoval" },
             mode: params.publish_dir_mode,
-            pattern: '*.fastq.gz'
+            pattern: '*.fastq.gz',
+            enabled: params.save_preprocessed_reads
         ]
     }
 
@@ -118,7 +117,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/adapterremoval" },
             mode: params.publish_dir_mode,
-            pattern: '*.fastq.gz'
+            pattern: '*.fastq.gz',
+            enabled: params.save_preprocessed_reads
         ]
     }
 
@@ -127,7 +127,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/porechop" },
             mode: params.publish_dir_mode,
-            pattern: '*.fastq.gz'
+            pattern: '*.fastq.gz',
+            enabled: params.save_preprocessed_reads
         ]
     }
 
@@ -141,7 +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
         ]
     }
 
@@ -154,7 +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
         ]
     }
 
diff --git a/nextflow.config b/nextflow.config
index e6d6307..19cc823 100644
--- a/nextflow.config
+++ b/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
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 6f6125e..6858409 100644
--- a/nextflow_schema.json
+++ b/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
         }
     }
 }