From d17dce5590d5b5c7366ebc5aa6f67331268e9a3d Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Tue, 7 Mar 2023 13:25:24 +0100
Subject: [PATCH] style: use subMap and early returns

---
 subworkflows/local/input_check.nf | 33 +++++++++++--------------------
 1 file changed, 12 insertions(+), 21 deletions(-)

diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
index e3cd0b4..37e3575 100644
--- a/subworkflows/local/input_check.nf
+++ b/subworkflows/local/input_check.nf
@@ -37,49 +37,40 @@ workflow INPUT_CHECK {
 // Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
 def create_fastq_channel(LinkedHashMap row) {
     // create meta map
-    def meta = [:]
-    meta.id                     = row.sample
-    meta.run_accession          = row.run_accession
-    meta.instrument_platform    = row.instrument_platform
-    meta.single_end             = row.single_end.toBoolean()
-    meta.is_fasta               = false
+    def meta = row.subMap(['sample', 'run_accession', 'instrument_platform'])
+    meta.single_end = row.single_end.toBoolean()
+    meta.is_fasta   = false
 
     // add path(s) of the fastq file(s) to the meta map
-    def fastq_meta = []
     if (!file(row.fastq_1).exists()) {
         exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}"
     }
+
     if (meta.single_end) {
-        fastq_meta = [ meta, [ file(row.fastq_1) ] ]
+        return [ meta, [ file(row.fastq_1) ] ]
     } else {
         if (meta.instrument_platform == 'OXFORD_NANOPORE') {
             if (row.fastq_2 != '') {
                 exit 1, "ERROR: Please check input samplesheet -> For Oxford Nanopore reads Read 2 FastQ should be empty!\n${row.fastq_2}"
             }
-            fastq_meta = [ meta, [ file(row.fastq_1) ] ]
+            return [ 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) ] ]
+            return [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
         }
-
     }
-    return fastq_meta
-}// Function to get list of [ meta, fasta ]
+}
+
+// Function to get list of [ meta, fasta ]
 def create_fasta_channel(LinkedHashMap row) {
-    def meta = [:]
-    meta.id                     = row.sample
-    meta.run_accession          = row.run_accession
-    meta.instrument_platform    = row.instrument_platform
+    def meta = row.subMap(['sample', 'run_accession', 'instrument_platform'])
     meta.single_end             = true
     meta.is_fasta               = true
 
-    def array = []
     if (!file(row.fasta).exists()) {
         exit 1, "ERROR: Please check input samplesheet -> FastA file does not exist!\n${row.fasta}"
     }
-    array = [ meta, [ file(row.fasta) ] ]
-
-    return array
+    return [ meta, [ file(row.fasta) ] ]
 }