From 40d520e3d642a0b85fcec8609af8fd1352c132a6 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 10 Jun 2021 14:43:32 +0100
Subject: [PATCH] Revert to conditional include in main script

---
 main.nf               |  7 +++++--
 workflows/illumina.nf | 12 ++++--------
 workflows/nanopore.nf | 12 ++++--------
 3 files changed, 13 insertions(+), 18 deletions(-)

diff --git a/main.nf b/main.nf
index 35f7dbd4..9d9eb79d 100644
--- a/main.nf
+++ b/main.nf
@@ -47,8 +47,11 @@ WorkflowMain.initialise(workflow, params, log)
 ========================================================================================
 */
 
-include { ILLUMINA } from './workflows/illumina'
-include { NANOPORE } from './workflows/nanopore'
+if (params.platform == 'illumina') {
+    include { ILLUMINA } from './workflows/illumina'
+} else if (params.platform == 'nanopore') {
+    include { NANOPORE } from './workflows/nanopore'
+}
 
 workflow NFCORE_VIRALRECON {
 
diff --git a/workflows/illumina.nf b/workflows/illumina.nf
index 1ca9562c..fabadb31 100644
--- a/workflows/illumina.nf
+++ b/workflows/illumina.nf
@@ -14,9 +14,7 @@ def valid_params = [
 def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
 
 // Validate input parameters
-if (params.platform == 'illumina') {
-    WorkflowIllumina.initialise(params, log, valid_params)
-}
+WorkflowIllumina.initialise(params, log, valid_params)
 
 // Check input path parameters to see if they exist
 def checkPathParamList = [
@@ -689,11 +687,9 @@ workflow ILLUMINA {
 ========================================================================================
 */
 
-if (params.platform == 'illumina') {
-    workflow.onComplete {
-        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report, fail_mapped_reads)
-        NfcoreTemplate.summary(workflow, params, log, fail_mapped_reads, pass_mapped_reads)
-    }
+workflow.onComplete {
+    NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report, fail_mapped_reads)
+    NfcoreTemplate.summary(workflow, params, log, fail_mapped_reads, pass_mapped_reads)
 }
 
 /*
diff --git a/workflows/nanopore.nf b/workflows/nanopore.nf
index 68af87f9..977b7d5b 100644
--- a/workflows/nanopore.nf
+++ b/workflows/nanopore.nf
@@ -12,9 +12,7 @@ def valid_params = [
 def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
 
 // Validate input parameters
-if (params.platform == 'nanopore') {
-    WorkflowNanopore.initialise(params, log, valid_params)
-}
+WorkflowNanopore.initialise(params, log, valid_params)
 
 def checkPathParamList = [
     params.input, params.fastq_dir, params.fast5_dir,
@@ -503,11 +501,9 @@ workflow NANOPORE {
 ========================================================================================
 */
 
-if (params.platform == 'nanopore') {
-    workflow.onComplete {
-        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
-        NfcoreTemplate.summary(workflow, params, log)
-    }
+workflow.onComplete {
+    NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
+    NfcoreTemplate.summary(workflow, params, log)
 }
 
 /*