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

@@ -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 \\

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

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() )
 
 }

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
+    - path: output/metaphlan3/test.txt
       contains: ["clade_name	NCBI_tax_id"]