From 5644df8d43b226281e21c3973940b31d1d6b9ce6 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 27 Jul 2022 15:19:43 +0200 Subject: [PATCH] Update module: Gecco fix to no file generated if no hits found (#1930) * Make gene and cluster TSVs optional output in case no hits found * update indicating optional output * Apply suggestions from code review Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com> Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com> --- modules/gecco/run/main.nf | 6 +++--- modules/gecco/run/meta.yml | 8 ++++---- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/modules/gecco/run/main.nf b/modules/gecco/run/main.nf index 7103250c..7bce527a 100644 --- a/modules/gecco/run/main.nf +++ b/modules/gecco/run/main.nf @@ -13,9 +13,9 @@ process GECCO_RUN { output: - tuple val(meta), path("*.genes.tsv") , emit: genes - tuple val(meta), path("*.features.tsv") , emit: features - tuple val(meta), path("*.clusters.tsv") , emit: clusters + tuple val(meta), path("*.genes.tsv") , optional: true, emit: genes + tuple val(meta), path("*.features.tsv") , emit: features + tuple val(meta), path("*.clusters.tsv") , optional: true, emit: clusters tuple val(meta), path("*_cluster_*.gbk"), optional: true, emit: gbk tuple val(meta), path("*.json") , optional: true, emit: json diff --git a/modules/gecco/run/meta.yml b/modules/gecco/run/meta.yml index bfa55586..24209719 100644 --- a/modules/gecco/run/meta.yml +++ b/modules/gecco/run/meta.yml @@ -44,7 +44,7 @@ output: pattern: "versions.yml" - genes: type: file - description: TSV file containing detected/predicted genes with BGC probability scores + description: TSV file containing detected/predicted genes with BGC probability scores. Will not be generated if no hits are found. pattern: "*.genes.tsv" - features: type: file @@ -52,15 +52,15 @@ output: pattern: "*.features.tsv" - clusters: type: file - description: TSV file containing coordinates of predicted clusters and BGC types + description: TSV file containing coordinates of predicted clusters and BGC types. Will not be generated if no hits are found. pattern: "*.clusters.tsv" - gbk: type: file - description: Per cluster GenBank file (if found) containing sequence with annotations + Description: Per cluster GenBank file (if found) containing sequence with annotations. Will not be generated if no hits are found. pattern: "*.gbk" - json: type: file - description: AntiSMASH v6 sideload JSON file (if --antismash-sideload) supplied + description: AntiSMASH v6 sideload JSON file (if --antismash-sideload) supplied. Will not be generated if no hits are found. pattern: "*.gbk" authors: