From 76cdd46f3f8a77fb5023fb5a39c4ab99925b8b56 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Thu, 3 Mar 2022 16:35:19 +0100
Subject: [PATCH] Add meta to MALT/RUN (#1372)

* Add meta to MALT/RUN

* Update modules/malt/run/main.nf
---
 modules/malt/run/main.nf       | 11 ++++++-----
 modules/malt/run/meta.yml      |  5 +++++
 tests/modules/malt/run/main.nf |  6 +++++-
 3 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/modules/malt/run/main.nf b/modules/malt/run/main.nf
index 99657305..61c02ec1 100644
--- a/modules/malt/run/main.nf
+++ b/modules/malt/run/main.nf
@@ -1,4 +1,5 @@
 process MALT_RUN {
+    tag "$meta.id"
     label 'process_high'
 
     conda (params.enable_conda ? "bioconda::malt=0.53" : null)
@@ -7,15 +8,15 @@ process MALT_RUN {
         'quay.io/biocontainers/malt:0.53--hdfd78af_0' }"
 
     input:
-    path fastqs
+    tuple val(meta), path(fastqs)
     val mode
     path index
 
     output:
-    path "*.rma6"                          , emit: rma6
-    path "*.{tab,text,sam}",  optional:true, emit: alignments
-    path "*.log"                           , emit: log
-    path "versions.yml"                    , emit: versions
+    tuple val(meta), path("*.rma6")                          , emit: rma6
+    tuple val(meta), path("*.{tab,text,sam}"),  optional:true, emit: alignments
+    tuple val(meta), path("*.log")                           , emit: log
+    path "versions.yml"                                      , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/malt/run/meta.yml b/modules/malt/run/meta.yml
index 7bd79290..ae4277a8 100644
--- a/modules/malt/run/meta.yml
+++ b/modules/malt/run/meta.yml
@@ -19,6 +19,11 @@ tools:
       licence: ["GPL v3"]
 
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - fastqs:
       type: file
       description: Input FASTQ files
diff --git a/tests/modules/malt/run/main.nf b/tests/modules/malt/run/main.nf
index 292a3fcf..d92dee71 100644
--- a/tests/modules/malt/run/main.nf
+++ b/tests/modules/malt/run/main.nf
@@ -12,10 +12,14 @@ workflow test_malt_run {
     gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
     seq_type = "DNA"
     map_db = file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true)
-    input = file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
     mode = "BlastN"
 
     UNZIP ( map_db )
     MALT_BUILD ( fastas, seq_type, gff, UNZIP.out.unzipped_archive )
     MALT_RUN ( input, mode, MALT_BUILD.out.index )
 }
+