From 36bcd675ae76a379a38165898a203f4915823f4f Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Tue, 13 Sep 2022 14:37:46 +0200
Subject: [PATCH] Update METAPHLAN3/MERGEMETAPHLANTABLES (#2041)

* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Add meta to mergemetaphlan3 tables

* Actually combine the data together
---
 modules/metaphlan3/mergemetaphlantables/main.nf        |  6 +++---
 modules/metaphlan3/mergemetaphlantables/meta.yml       | 10 ++++++++++
 tests/modules/metaphlan3/mergemetaphlantables/main.nf  |  2 +-
 tests/modules/metaphlan3/mergemetaphlantables/test.yml |  6 +++---
 4 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/modules/metaphlan3/mergemetaphlantables/main.nf b/modules/metaphlan3/mergemetaphlantables/main.nf
index 6fd05e3a..7c37ecab 100644
--- a/modules/metaphlan3/mergemetaphlantables/main.nf
+++ b/modules/metaphlan3/mergemetaphlantables/main.nf
@@ -7,10 +7,10 @@ process METAPHLAN3_MERGEMETAPHLANTABLES {
         'quay.io/biocontainers/metaphlan:3.0.12--pyhb7b1952_0' }"
 
     input:
-    path(profiles)
+    tuple val(meta), path(profiles)
 
     output:
-    tuple path("${prefix}.txt") , emit: txt
+    tuple val(meta), path("${prefix}.txt") , emit: txt
     path "versions.yml" , emit: versions
 
     when:
@@ -18,7 +18,7 @@ process METAPHLAN3_MERGEMETAPHLANTABLES {
 
     script:
     def args = task.ext.args ?: ''
-    prefix = task.ext.prefix ?: "merged_abundance_table"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     merge_metaphlan_tables.py \\
         $args \\
diff --git a/modules/metaphlan3/mergemetaphlantables/meta.yml b/modules/metaphlan3/mergemetaphlantables/meta.yml
index c94be25c..365973ef 100644
--- a/modules/metaphlan3/mergemetaphlantables/meta.yml
+++ b/modules/metaphlan3/mergemetaphlantables/meta.yml
@@ -15,12 +15,22 @@ tools:
       licence: ["MIT License"]
 
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - profiles:
       type: file
       description: List of per-sample MetaPhlAn3 taxonomic abundance tables
       pattern: "*"
 
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - versions:
       type: file
       description: File containing software versions
diff --git a/tests/modules/metaphlan3/mergemetaphlantables/main.nf b/tests/modules/metaphlan3/mergemetaphlantables/main.nf
index dd99c6c3..6a158d6a 100644
--- a/tests/modules/metaphlan3/mergemetaphlantables/main.nf
+++ b/tests/modules/metaphlan3/mergemetaphlantables/main.nf
@@ -17,6 +17,6 @@ workflow test_metaphlan3_mergemetaphlantables {
 
     UNTAR ( db )
     METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
-    METAPHLAN3_MERGEMETAPHLANTABLES ( METAPHLAN3.out.profile.map{it[1]}.collect() )
+    METAPHLAN3_MERGEMETAPHLANTABLES ( METAPHLAN3.out.profile.map{ [[id:"test"], it[1]] }.groupTuple() )
 
 }
diff --git a/tests/modules/metaphlan3/mergemetaphlantables/test.yml b/tests/modules/metaphlan3/mergemetaphlantables/test.yml
index 55690861..57b69aa5 100644
--- a/tests/modules/metaphlan3/mergemetaphlantables/test.yml
+++ b/tests/modules/metaphlan3/mergemetaphlantables/test.yml
@@ -1,8 +1,8 @@
 - name: metaphlan3 mergemetaphlantables test_metaphlan3_mergemetaphlantables
   command: nextflow run ./tests/modules/metaphlan3/mergemetaphlantables -entry test_metaphlan3_mergemetaphlantables -c ./tests/config/nextflow.config  -c ./tests/modules/metaphlan3/mergemetaphlantables/nextflow.config
   tags:
-    - metaphlan3
     - metaphlan3/mergemetaphlantables
+    - metaphlan3
   files:
-    - path: output/metaphlan3/merged_abundance_table.txt
-      contains: ["clade_name	NCBI_tax_id	"]
+    - path: output/metaphlan3/test.txt
+      contains: ["clade_name	NCBI_tax_id"]