From b5a2983c5f6fa148f4ceb9824b77f05d5bfea9a4 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 7 Mar 2023 11:06:35 +0100
Subject: [PATCH] Make modules entries consistent

---
 conf/modules.config | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 41b3717..e74e1a9 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -196,8 +196,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/bowtie2/build" },
             mode: params.publish_dir_mode,
-            enabled: params.save_hostremoval_index,
-            pattern: 'bowtie2'
+            pattern: 'bowtie2',
+            enabled: params.save_hostremoval_index
         ]
     }
 
@@ -213,14 +213,14 @@ process {
             [
                 path: { "${params.outdir}/bowtie2/align" },
                 mode: params.publish_dir_mode,
-                enabled: params.save_hostremoval_bam,
-                pattern: '*.bam'
+                pattern: '*.bam',
+                enabled: params.save_hostremoval_bam
             ],
             [
                 path: { "${params.outdir}/bowtie2/align" },
                 mode: params.publish_dir_mode,
-                enabled: params.save_hostremoval_unmapped,
-                pattern: '*.fastq.gz'
+                pattern: '*.fastq.gz',
+                enabled: params.save_hostremoval_unmapped
             ]
         ]
     }
@@ -230,8 +230,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/minimap2/index" },
             mode: params.publish_dir_mode,
-            enabled: params.save_hostremoval_index,
-            pattern: '*.mmi'
+            pattern: '*.mmi',
+            enabled: params.save_hostremoval_index
         ]
     }
 
@@ -240,8 +240,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/minimap2/align" },
             mode: params.publish_dir_mode,
-            enabled: params.save_hostremoval_bam,
-            pattern: '*.bam'
+            pattern: '*.bam',
+            enabled: params.save_hostremoval_bam
         ]
     }
 
@@ -255,8 +255,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/samtools/bam2fq" },
             mode: params.publish_dir_mode,
-            enabled: params.save_hostremoval_unmapped,
-            pattern: '*.fq.gz'
+            pattern: '*.fq.gz',
+            enabled: params.save_hostremoval_unmapped
         ]
     }
 
@@ -446,13 +446,13 @@ process {
     }
 
     withName: CENTRIFUGE_CENTRIFUGE {
+        ext.args = { "${meta.db_params}" }
+        ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
         publishDir = [
             path: { "${params.outdir}/centrifuge/${meta.db_name}/" },
             mode: params.publish_dir_mode,
             pattern: '*.{txt,sam,gz}'
         ]
-        ext.args = { "${meta.db_params}" }
-        ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
     }
 
     withName: CENTRIFUGE_KREPORT {
@@ -477,13 +477,13 @@ process {
     }
 
     withName: KAIJU_KAIJU {
+        ext.args = { "${meta.db_params}" }
         ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kaiju" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kaiju" }
         publishDir = [
             path: { "${params.outdir}/kaiju/${meta.db_name}/" },
             mode: params.publish_dir_mode,
             pattern: '*.tsv'
         ]
-        ext.args = { "${meta.db_params}" }
     }
 
     withName: 'KAIJU_KAIJU2TABLE_SINGLE' {