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Update mOTUs to remove now unused channel (#2075)

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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

* Update main.nf

* Remove now unnecessary input channel

* Remove unused channel from tests
This commit is contained in:
James A. Fellows Yates 2022-09-16 10:23:21 +02:00 committed by GitHub
parent b121596ae0
commit 54ff289487
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3 changed files with 2 additions and 6 deletions
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1
modules/motus/merge/main.nf
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@ -13,7 +13,6 @@ process MOTUS_MERGE {
tuple val(meta), 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 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' path profile_version_yml, stageAs: 'profile_version.yml'
val biom_format
output: output:
tuple val(meta), path("*.txt") , optional: true, emit: txt tuple val(meta), path("*.txt") , optional: true, emit: txt

3
modules/motus/merge/meta.yml
View file

@ -35,9 +35,6 @@ input:
this itself without having the motus database present and configured with the tool this itself without having the motus database present and configured with the tool
so here we take it from what is already reported by the upstream module. so here we take it from what is already reported by the upstream module.
pattern: "versions.yml" pattern: "versions.yml"
- biom_format:
type: boolean
description: Whether to save output OTU table in biom format
output: output:
- versions: - versions:

4
tests/modules/motus/merge/main.nf
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@ -24,7 +24,7 @@ workflow test_motus_merge {
MOTUS_DOWNLOADDB ( file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py') ) MOTUS_DOWNLOADDB ( file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py') )
MOTUS_PROFILE ( input, MOTUS_DOWNLOADDB.out.db ) MOTUS_PROFILE ( input, MOTUS_DOWNLOADDB.out.db )
MOTUS_MERGE ( MOTUS_PROFILE.out.out.map{ [[id:"test"], it[1]] }.groupTuple(), 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() )
} }
@ -45,7 +45,7 @@ workflow test_motus_merge_biom {
MOTUS_DOWNLOADDB ( file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py') ) MOTUS_DOWNLOADDB ( file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py') )
MOTUS_PROFILE ( input, MOTUS_DOWNLOADDB.out.db ) 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 ) MOTUS_MERGE_BIOM ( MOTUS_PROFILE.out.out.map{ [[id:"test"], it[1]] }.groupTuple(), MOTUS_DOWNLOADDB.out.db, MOTUS_PROFILE.out.versions.first() )
} }