From 54ff289487244bf15543ecfa62bd4df49be72b73 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 16 Sep 2022 10:23:21 +0200 Subject: [PATCH] Update mOTUs to remove now unused channel (#2075) * 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 --- modules/motus/merge/main.nf | 1 - modules/motus/merge/meta.yml | 3 --- tests/modules/motus/merge/main.nf | 4 ++-- 3 files changed, 2 insertions(+), 6 deletions(-) diff --git a/modules/motus/merge/main.nf b/modules/motus/merge/main.nf index dcab92f0..a050c7ae 100644 --- a/modules/motus/merge/main.nf +++ b/modules/motus/merge/main.nf @@ -13,7 +13,6 @@ process MOTUS_MERGE { 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: tuple val(meta), path("*.txt") , optional: true, emit: txt diff --git a/modules/motus/merge/meta.yml b/modules/motus/merge/meta.yml index c9c7711f..02d11d04 100644 --- a/modules/motus/merge/meta.yml +++ b/modules/motus/merge/meta.yml @@ -35,9 +35,6 @@ input: 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. pattern: "versions.yml" - - biom_format: - type: boolean - description: Whether to save output OTU table in biom format output: - versions: diff --git a/tests/modules/motus/merge/main.nf b/tests/modules/motus/merge/main.nf index 99b19f56..bb1b7150 100644 --- a/tests/modules/motus/merge/main.nf +++ b/tests/modules/motus/merge/main.nf @@ -24,7 +24,7 @@ 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{ [[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_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() ) }