From 7c74c5c4f6650a4f6adc6fd870b72887252fe34e Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 27 Jul 2023 13:36:25 +0200 Subject: [PATCH] Improve output glob for optional alignments --- modules/nf-core/centrifuge/centrifuge/main.nf | 2 +- modules/nf-core/centrifuge/centrifuge/meta.yml | 5 +++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf index 953705b659b..964ee2cdfff 100644 --- a/modules/nf-core/centrifuge/centrifuge/main.nf +++ b/modules/nf-core/centrifuge/centrifuge/main.nf @@ -16,7 +16,7 @@ process CENTRIFUGE_CENTRIFUGE { output: tuple val(meta), path('*report.txt') , emit: report tuple val(meta), path('*results.txt') , emit: results - tuple val(meta), path('*.sam') , optional: true, emit: sam + tuple val(meta), path('*.{sam,tab}') , optional: true, emit: sam tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_mapped tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped path "versions.yml" , emit: versions diff --git a/modules/nf-core/centrifuge/centrifuge/meta.yml b/modules/nf-core/centrifuge/centrifuge/meta.yml index a252c00c2ce..4814637065f 100644 --- a/modules/nf-core/centrifuge/centrifuge/meta.yml +++ b/modules/nf-core/centrifuge/centrifuge/meta.yml @@ -48,6 +48,11 @@ output: description: | File containing classification results pattern: "*.{results.txt}" + - sam: + type: file + description: | + Optional output file containing read alignments (SAM format )or a table of per-read hit information (TAB)s + pattern: "*.{sam,tab}" - fastq_unmapped: type: file description: Unmapped fastq files