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Update module: Gecco fix to no file generated if no hits found (#1930)

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* 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>
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James A. Fellows Yates 2022-07-27 15:19:43 +02:00 committed by GitHub
parent 734d0db607
commit 5644df8d43
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2 changed files with 7 additions and 7 deletions
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4
modules/gecco/run/main.nf
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@ -13,9 +13,9 @@ process GECCO_RUN {
output: output:
tuple val(meta), path("*.genes.tsv") , emit: genes tuple val(meta), path("*.genes.tsv") , optional: true, emit: genes
tuple val(meta), path("*.features.tsv") , emit: features tuple val(meta), path("*.features.tsv") , emit: features
tuple val(meta), path("*.clusters.tsv") , emit: clusters tuple val(meta), path("*.clusters.tsv") , optional: true, emit: clusters
tuple val(meta), path("*_cluster_*.gbk"), optional: true, emit: gbk tuple val(meta), path("*_cluster_*.gbk"), optional: true, emit: gbk
tuple val(meta), path("*.json") , optional: true, emit: json tuple val(meta), path("*.json") , optional: true, emit: json

8
modules/gecco/run/meta.yml
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@ -44,7 +44,7 @@ output:
pattern: "versions.yml" pattern: "versions.yml"
- genes: - genes:
type: file 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" pattern: "*.genes.tsv"
- features: - features:
type: file type: file
@ -52,15 +52,15 @@ output:
pattern: "*.features.tsv" pattern: "*.features.tsv"
- clusters: - clusters:
type: file 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" pattern: "*.clusters.tsv"
- gbk: - gbk:
type: file 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" pattern: "*.gbk"
- json: - json:
type: file 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" pattern: "*.gbk"
authors: authors: