From d94534e8acee01575b589e88549ed64ab4fc4411 Mon Sep 17 00:00:00 2001
From: ljmesi <37740329+ljmesi@users.noreply.github.com>
Date: Thu, 5 May 2022 09:07:33 +0200
Subject: [PATCH] Simplify params which control host removal publish

---
 conf/modules.config  |  8 ++++----
 nextflow.config      |  6 +-----
 nextflow_schema.json | 16 ----------------
 3 files changed, 5 insertions(+), 25 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index b707954..cd0fb04 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -169,7 +169,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/minimap2/index" },
             mode: params.publish_dir_mode,
-            enabled: params.save_minimap2_hostremoval_index,
+            enabled: params.save_hostremoval_index,
             pattern: 'minimap2'
         ]
     }
@@ -179,7 +179,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/minimap2/align" },
             mode: params.publish_dir_mode,
-            enabled: params.save_minimap2_hostremoval_mapped,
+            enabled: params.save_hostremoval_mapped,
             pattern: '*.bam'
         ]
     }
@@ -190,7 +190,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/samtools/view" },
             mode: params.publish_dir_mode,
-            enabled: params.save_samtools_unmapped_bam,
+            enabled: params.save_hostremoval_unmapped,
             pattern: '*.bam'
         ]
     }
@@ -200,7 +200,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/samtools/bam2fq" },
             mode: params.publish_dir_mode,
-            enabled: params.save_minimap2_unmapped_fq,
+            enabled: params.save_hostremoval_unmapped,
             pattern: '*.fq.gz'
         ]
     }
diff --git a/nextflow.config b/nextflow.config
index 95daba9..8c99af2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -84,14 +84,10 @@ params {
     perform_shortread_hostremoval          = false
     shortread_hostremoval_reference        = null
     shortread_hostremoval_index            = null
+    longread_hostremoval_index             = null
     save_hostremoval_index                 = false
     save_hostremoval_mapped                = false
     save_hostremoval_unmapped              = false
-    longread_hostremoval_index             = null
-    save_minimap2_hostremoval_index        = false
-    save_minimap2_hostremoval_mapped       = false
-    save_samtools_unmapped_bam             = false
-    save_minimap2_unmapped_fq              = false
 
 
     // MALT
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 1902e27..9e4cc6c 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -401,22 +401,6 @@
         "longread_hostremoval_index": {
             "type": "string",
             "default": "None"
-        },
-        "save_minimap2_hostremoval_index": {
-            "type": "boolean",
-            "description": "Flag for publishing minimap2 host removal index"
-        },
-        "save_minimap2_hostremoval_mapped": {
-            "type": "boolean",
-            "description": "Flag for publishinig bam file with all long reads mapped to a reference"
-        },
-        "save_samtools_unmapped_bam": {
-            "type": "boolean",
-            "description": "Flag for publishing bam for reads that did not map to the host reference"
-        },
-        "save_minimap2_unmapped_fq": {
-            "type": "boolean",
-            "description": "Flag for publishing fastq files for reads that did not map to the host reference"
         }
     }
 }