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Update motus merge module to remove unused channel

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This commit is contained in:
James Fellows Yates 2022-09-16 10:25:24 +02:00
parent 4e7857e2ed
commit c5cc21d29e
4 changed files with 2 additions and 6 deletions
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2
modules.json
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@ -111,7 +111,7 @@
}, },
"motus/merge": { "motus/merge": {
"branch": "master", "branch": "master",
"git_sha": "8372df6fb2a7638adacae070860685373be61e1f" "git_sha": "54ff289487244bf15543ecfa62bd4df49be72b73"
}, },
"motus/profile": { "motus/profile": {
"branch": "master", "branch": "master",

1
modules/nf-core/modules/motus/merge/main.nf generated
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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/nf-core/modules/motus/merge/meta.yml generated
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@ -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:

2
subworkflows/local/standardisation_profiles.nf
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@ -109,7 +109,7 @@ workflow STANDARDISATION_PROFILES {
[[id:it[0]], it[1]] [[id:it[0]], it[1]]
} }
MOTUS_MERGE ( ch_profiles_for_motus, ch_input_databases.motus.map{it[1]}, motu_version, [] ) MOTUS_MERGE ( ch_profiles_for_motus, ch_input_databases.motus.map{it[1]}, motu_version )
if ( params.generate_biom_output ) { if ( params.generate_biom_output ) {
ch_standardised_tables = ch_standardised_tables.mix ( MOTUS_MERGE.out.biom ) ch_standardised_tables = ch_standardised_tables.mix ( MOTUS_MERGE.out.biom )