From 41b3d8db822caab916ec82fe4b4f581f17ab1ca5 Mon Sep 17 00:00:00 2001
From: ljmesi <37740329+ljmesi@users.noreply.github.com>
Date: Fri, 18 Mar 2022 10:47:41 +0100
Subject: [PATCH] Add nanopore channel

---
 subworkflows/local/input_check.nf | 21 +++++++++++++++++----
 1 file changed, 17 insertions(+), 4 deletions(-)

diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
index 481028f..2e30bcc 100644
--- a/subworkflows/local/input_check.nf
+++ b/subworkflows/local/input_check.nf
@@ -20,10 +20,15 @@ workflow INPUT_CHECK {
         }
 
     parsed_samplesheet.fastq
-        .map { create_fastq_channels(it) }
+        .map { create_fastq_channel(it) }
         .dump(tag: "fastq_channel_init")
         .set { fastq }
 
+    parsed_samplesheet.nanopore
+        .map { create_fastq_channel(it) }
+        .dump(tag: "fastq_nanopore_channel_init")
+        .set { nanopore }
+
     parsed_samplesheet.fasta
         .map { create_fasta_channels(it) }
         .dump(tag: "fasta_channel_init")
@@ -31,6 +36,7 @@ workflow INPUT_CHECK {
 
     emit:
     fastq                                     // channel: [ val(meta), [ reads ] ]
+    nanopore                                  // channel: [ val(meta), [ reads ] ]
     fasta                                     // channel: [ val(meta), fasta ]
     versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ]
 }
@@ -52,10 +58,17 @@ def create_fastq_channel(LinkedHashMap row) {
     if (meta.single_end) {
         fastq_meta = [ meta, [ file(row.fastq_1) ] ]
     } else {
-        if (!file(row.fastq_2).exists()) {
-            exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
+        if (meta.instrument_platform == 'OXFORD_NANOPORE') {
+            if (row.fastq_2 != '') {
+                exit 1, "ERROR: Please check input samplesheet -> For Oxford Nanopore reads Read 2 FastQ should be empty!\n${row.fastq_2}"
+            }
+            fastq_meta = [ meta, [ file(row.fastq_1) ] ]
+        } else {
+            if (!file(row.fastq_2).exists()) {
+                exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
+            }
+            fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
         }
-        fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
     }
     return fastq_meta
 }