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Update METAPHLAN3_METAPHLAN3 to correct module name (#2056)

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* 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
This commit is contained in:
James A. Fellows Yates 2022-09-15 09:09:55 +02:00 committed by GitHub
parent 885e724e07
commit 978087354e
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5 changed files with 14 additions and 14 deletions
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2
modules/metaphlan3/metaphlan3/main.nf
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@ -1,4 +1,4 @@
process METAPHLAN3 { process METAPHLAN3_METAPHLAN3 {
tag "$meta.id" tag "$meta.id"
label 'process_high' label 'process_high'

2
modules/metaphlan3/metaphlan3/meta.yml
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@ -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. description: MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
keywords: keywords:
- metagenomics - metagenomics

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

2
tests/modules/metaphlan3/metaphlan3/nextflow.config
View file

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

8
tests/modules/metaphlan3/metaphlan3/test.yml
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@ -1,5 +1,5 @@
- name: metaphlan3 test_metaphlan3_single_end - 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: tags:
- metaphlan3 - metaphlan3
files: files:
@ -30,7 +30,7 @@
md5sum: 1ca16b905abf657b88ca2bc12e7ad404 md5sum: 1ca16b905abf657b88ca2bc12e7ad404
- name: metaphlan3 test_metaphlan3_paired_end - 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: tags:
- metaphlan3 - metaphlan3
files: files:
@ -61,7 +61,7 @@
md5sum: 1ca16b905abf657b88ca2bc12e7ad404 md5sum: 1ca16b905abf657b88ca2bc12e7ad404
- name: metaphlan3 test_metaphlan3_sam - 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: tags:
- metaphlan3 - metaphlan3
files: files:
@ -92,7 +92,7 @@
md5sum: 1ca16b905abf657b88ca2bc12e7ad404 md5sum: 1ca16b905abf657b88ca2bc12e7ad404
- name: metaphlan3 test_metaphlan3_fasta - 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: tags:
- metaphlan3 - metaphlan3
files: files: