Update METAPHLAN3_METAPHLAN3 to correct module name (#2056)

* Update main.nf

* Update meta.yml

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

* Fix MeaPhlAn3 module name

* Fix metayaml

* Fix meta.yml

modules/metaphlan3/metaphlan3/main.nf

@@ -1,4 +1,4 @@
-process METAPHLAN3 {
+process METAPHLAN3_METAPHLAN3 {
     tag "$meta.id"
     label 'process_high'
 

modules/metaphlan3/metaphlan3/meta.yml

@@ -1,4 +1,4 @@
-name: metaphlan3
+name: metaphlan3_metaphlan3
 description: MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
 keywords:
   - metagenomics

tests/modules/metaphlan3/metaphlan3/main.nf

@@ -2,8 +2,8 @@
 
 nextflow.enable.dsl = 2
 
-include { UNTAR          } from '../../../../modules/untar/main.nf'
-include { METAPHLAN3     } from '../../../../modules/metaphlan3/metaphlan3/main.nf'
+include { UNTAR                 } from '../../../../modules/untar/main.nf'
+include { METAPHLAN3_METAPHLAN3 } from '../../../../modules/metaphlan3/metaphlan3/main.nf'
 
 workflow test_metaphlan3_single_end {
 
@@ -14,7 +14,7 @@ workflow test_metaphlan3_single_end {
     db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
 
     UNTAR ( db )
-    METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
+    METAPHLAN3_METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
 }
 
 workflow test_metaphlan3_single_end_nodb {
@@ -24,7 +24,7 @@ workflow test_metaphlan3_single_end_nodb {
             ]
 
     UNTAR ( db )
-    METAPHLAN3 ( input, [] )
+    METAPHLAN3_METAPHLAN3 ( input, [] )
 }
 
 workflow test_metaphlan3_paired_end {
@@ -37,7 +37,7 @@ workflow test_metaphlan3_paired_end {
     db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
 
     UNTAR ( db )
-    METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
+    METAPHLAN3_METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
 }
 
 workflow test_metaphlan3_sam {
@@ -50,7 +50,7 @@ workflow test_metaphlan3_sam {
 
     UNTAR ( db )
     SAMTOOLS_VIEW ( input, [] )
-    METAPHLAN3 ( SAMTOOLS_VIEW.out.bam, UNTAR.out.untar.map{ it[1] } )
+    METAPHLAN3_METAPHLAN3 ( SAMTOOLS_VIEW.out.bam, UNTAR.out.untar.map{ it[1] } )
 }
 
 workflow test_metaphlan3_fasta {
@@ -62,5 +62,5 @@ workflow test_metaphlan3_fasta {
     db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
 
     UNTAR ( db )
-    METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
+    METAPHLAN3_METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
 }

tests/modules/metaphlan3/metaphlan3/nextflow.config

@@ -2,7 +2,7 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
-    withName: METAPHLAN3 {
+    withName: METAPHLAN3_METAPHLAN3 {
         ext.args = '--index mpa_v30_CHOCOPhlAn_201901 --add_viruses --bt2_ps very-sensitive-local'
     }
 

tests/modules/metaphlan3/metaphlan3/test.yml

@@ -1,5 +1,5 @@
 - name: metaphlan3 test_metaphlan3_single_end
-  command: nextflow run ./tests/modules/metaphlan3 -entry test_metaphlan3_single_end -c ./tests/config/nextflow.config -c ./tests/modules/metaphlan3/nextflow.config
+  command: nextflow run ./tests/modules/metaphlan3/metaphlan3 -entry test_metaphlan3_single_end -c ./tests/config/nextflow.config -c ./tests/modules/metaphlan3/metaphlan3/nextflow.config
   tags:
     - metaphlan3
   files:
@@ -30,7 +30,7 @@
       md5sum: 1ca16b905abf657b88ca2bc12e7ad404
 
 - name: metaphlan3 test_metaphlan3_paired_end
-  command: nextflow run ./tests/modules/metaphlan3 -entry test_metaphlan3_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/metaphlan3/nextflow.config
+  command: nextflow run ./tests/modules/metaphlan3/metaphlan3 -entry test_metaphlan3_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/metaphlan3/metaphlan3/nextflow.config
   tags:
     - metaphlan3
   files:
@@ -61,7 +61,7 @@
       md5sum: 1ca16b905abf657b88ca2bc12e7ad404
 
 - name: metaphlan3 test_metaphlan3_sam
-  command: nextflow run ./tests/modules/metaphlan3 -entry test_metaphlan3_sam -c ./tests/config/nextflow.config -c ./tests/modules/metaphlan3/nextflow.config
+  command: nextflow run ./tests/modules/metaphlan3/metaphlan3 -entry test_metaphlan3_sam -c ./tests/config/nextflow.config -c ./tests/modules/metaphlan3/metaphlan3/nextflow.config
   tags:
     - metaphlan3
   files:
@@ -92,7 +92,7 @@
       md5sum: 1ca16b905abf657b88ca2bc12e7ad404
 
 - name: metaphlan3 test_metaphlan3_fasta
-  command: nextflow run ./tests/modules/metaphlan3 -entry test_metaphlan3_fasta -c ./tests/config/nextflow.config -c ./tests/modules/metaphlan3/nextflow.config
+  command: nextflow run ./tests/modules/metaphlan3/metaphlan3 -entry test_metaphlan3_fasta -c ./tests/config/nextflow.config -c ./tests/modules/metaphlan3/metaphlan3/nextflow.config
   tags:
     - metaphlan3
   files: