From 515793c73e7f1d8a742aad0ab830ad9575318784 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Mon, 4 Oct 2021 12:37:21 +0100
Subject: [PATCH] Fix bug with SortMeRna not working on a single db file (#788)

* Fix bug with SortMeRna not working on a single db file

* Remove tag for instances when running just to create index
---
 modules/bbmap/bbsplit/main.nf |  1 -
 modules/sortmerna/main.nf     | 11 ++++-------
 2 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/modules/bbmap/bbsplit/main.nf b/modules/bbmap/bbsplit/main.nf
index 7a24312b..b2249b17 100644
--- a/modules/bbmap/bbsplit/main.nf
+++ b/modules/bbmap/bbsplit/main.nf
@@ -5,7 +5,6 @@ params.options = [:]
 options        = initOptions(params.options)
 
 process BBMAP_BBSPLIT {
-    tag "$meta.id"
     label 'process_high'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
diff --git a/modules/sortmerna/main.nf b/modules/sortmerna/main.nf
index f35b1468..96fd06aa 100644
--- a/modules/sortmerna/main.nf
+++ b/modules/sortmerna/main.nf
@@ -20,7 +20,7 @@ process SORTMERNA {
 
     input:
     tuple val(meta), path(reads)
-    path  fasta
+    path  fastas
 
     output:
     tuple val(meta), path("*.fastq.gz"), emit: reads
@@ -28,14 +28,11 @@ process SORTMERNA {
     path  "versions.yml"               , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-
-    def Refs = ""
-    for (i=0; i<fasta.size(); i++) { Refs+= " --ref ${fasta[i]}" }
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     if (meta.single_end) {
         """
         sortmerna \\
-            $Refs \\
+            ${'--ref '+fastas.join(' --ref ')} \\
             --reads $reads \\
             --threads $task.cpus \\
             --workdir . \\
@@ -54,7 +51,7 @@ process SORTMERNA {
     } else {
         """
         sortmerna \\
-            $Refs \\
+            ${'--ref '+fastas.join(' --ref ')} \\
             --reads ${reads[0]} \\
             --reads ${reads[1]} \\
             --threads $task.cpus \\