From dd18de6c8fd5c53a347a4996f9497897e233b377 Mon Sep 17 00:00:00 2001
From: LilyAnderssonLee <lilili2011me@gmail.com>
Date: Thu, 6 Jul 2023 12:55:45 +0200
Subject: [PATCH] correct --input_type

---
 modules/nf-core/metaphlan/metaphlan/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/metaphlan/metaphlan/main.nf b/modules/nf-core/metaphlan/metaphlan/main.nf
index 3eb60f64780..477f1f28ddd 100644
--- a/modules/nf-core/metaphlan/metaphlan/main.nf
+++ b/modules/nf-core/metaphlan/metaphlan/main.nf
@@ -23,7 +23,7 @@ process METAPHLAN_METAPHLAN {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def input_type  = ("$input".endsWith(".fastq.gz") || "$input".endsWith(".fq.gz")) ? "--input_type fastq" :  ("$input".contains(".fasta")|| "$input".endsWith(".fa.gz")) ? "--input_type fasta" : ("$input".endsWith(".bowtie2out.txt")) ? "--input_type bowtie2out" : "--input_type sam"
+    def input_type = "$input" =~ /.*\.(fastq|fq)/ ? "--input_type fastq" : "$input" =~ /.*\.(fasta|fna|fa)/ ? "--input_type fasta" : "$input".endsWith(".bowtie2out.txt") ? "--input_type bowtie2out" : "--input_type sam"
     def input_data  = ("$input_type".contains("fastq")) && !meta.single_end ? "${input[0]},${input[1]}" : "$input"
     def bowtie2_out = "$input_type" == "--input_type bowtie2out" || "$input_type" == "--input_type sam" ? '' : "--bowtie2out ${prefix}.bowtie2out.txt"