Update MOTUS/MERGE (#2068)

* Update main.nf

* Update meta.yml

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

* Add meta to mOTUs merge

* Put tests back to use downloaded db

* Apply suggestions from code review

* Fix test text string

* md5sum -> contains

* Update nextflow.config

modules/motus/merge/main.nf

@@ -1,6 +1,7 @@
 VERSION = '3.0.1'
 
 process MOTUS_MERGE {
+    tag "$meta.id"
     label 'process_low'
 
     conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
@@ -9,14 +10,14 @@ process MOTUS_MERGE {
         'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
 
     input:
-    path input
+    tuple val(meta), path(input)
     path db // to stop docker saying it can't find it... would have to have the module in upstream steps anyway
     path profile_version_yml, stageAs: 'profile_version.yml'
     val biom_format
 
     output:
-    path("*.txt") , optional: true, emit: txt
-    path("*.biom"), optional: true, emit: biom
+    tuple val(meta), path("*.txt") , optional: true, emit: txt
+    tuple val(meta), path("*.biom"), optional: true, emit: biom
     path "versions.yml" , emit: versions
 
     when:
@@ -24,16 +25,16 @@ process MOTUS_MERGE {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = 'motus_merged'
+    def prefix = task.ext.prefix ?: "${meta.id}"
     def cmd_input = input.size() > 1 ? "-i ${input.join(',')}" : input.isDirectory() ? "-d ${input}" : "-i ${input}"
-    def output = biom_format ? "-B -o ${prefix}.biom" : "-o ${prefix}.txt"
+    def suffix = task.ext.args?.contains("-B") ? "biom" : "txt"
     """
     motus \\
         merge \\
         -db $db \\
         ${cmd_input} \\
         $args \\
-        ${output}
+        -o ${prefix}.${suffix}
 
     ## Take version from the mOTUs/profile module output, as cannot reconstruct
     ## version without having database staged in this directory.

tests/modules/motus/merge/main.nf

@@ -2,9 +2,10 @@
 
 nextflow.enable.dsl = 2
 
-include { MOTUS_DOWNLOADDB } from '../../../../modules/motus/downloaddb/main.nf'
-include { MOTUS_PROFILE    } from '../../../../modules/motus/profile/main.nf'
-include { MOTUS_MERGE } from '../../../../modules/motus/merge/main.nf'
+include { MOTUS_DOWNLOADDB                } from '../../../../modules/motus/downloaddb/main.nf'
+include { MOTUS_PROFILE                   } from '../../../../modules/motus/profile/main.nf'
+include { MOTUS_MERGE                     } from '../../../../modules/motus/merge/main.nf'
+include { MOTUS_MERGE as MOTUS_MERGE_BIOM } from '../../../../modules/motus/merge/main.nf'
 
 workflow test_motus_merge {
 
@@ -23,7 +24,28 @@ workflow test_motus_merge {
 
     MOTUS_DOWNLOADDB ( file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py') )
     MOTUS_PROFILE ( input, MOTUS_DOWNLOADDB.out.db )
-    MOTUS_MERGE ( MOTUS_PROFILE.out.out.map{it[1]}.collect(), MOTUS_DOWNLOADDB.out.db, MOTUS_PROFILE.out.versions.first(), false )
+    MOTUS_MERGE ( MOTUS_PROFILE.out.out.map{ [[id:"test"], it[1]] }.groupTuple(), MOTUS_DOWNLOADDB.out.db, MOTUS_PROFILE.out.versions.first(), false )
+
+}
+
+workflow test_motus_merge_biom {
+
+    input = Channel.fromList(
+        [
+            [
+                [ id:'test', single_end:true ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+            ],
+            [
+                [ id:'test2', single_end:true ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+            ]
+        ]
+    )
+
+    MOTUS_DOWNLOADDB ( file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py') )
+    MOTUS_PROFILE ( input, MOTUS_DOWNLOADDB.out.db )
+    MOTUS_MERGE_BIOM ( MOTUS_PROFILE.out.out.map{ [[id:"test"], it[1]] }.groupTuple(), MOTUS_DOWNLOADDB.out.db, MOTUS_PROFILE.out.versions.first(), false )
 
 }
 

tests/modules/motus/merge/nextflow.config

@@ -1,5 +1,8 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
+
+    withName: MOTUS_MERGE_BIOM {
+        ext.args = "-B"
+    }
+}

tests/modules/motus/merge/test.yml

@@ -4,9 +4,16 @@
     - motus
     - motus/merge
   files:
-    - path: output/motus/motus_merged.txt
-      contains: ["#consensus_taxonomy"]
-    - path: output/motus/test.out
-      contains: ["#consensus_taxonomy"]
-    - path: output/motus/test2.out
-      contains: ["#consensus_taxonomy"]
+    - path: output/motus/test.txt
+      contains:
+        - "consensus_taxonomy"
+
+- name: motus merge test_motus_merge_biom
+  command: nextflow run ./tests/modules/motus/merge -entry test_motus_merge_biom -c ./tests/config/nextflow.config  -c ./tests/modules/motus/merge/nextflow.config
+  tags:
+    - motus
+    - motus/merge
+  files:
+    - path: output/motus/test.biom
+      contains:
+        - "Biological Observation Matrix 1.0.0"