From 75fab2fc7171f25c356bc8dd8064e64ceb0ec67c Mon Sep 17 00:00:00 2001 From: julicudini Date: Wed, 14 Aug 2024 11:10:20 +0100 Subject: [PATCH] expand subdir search to capture fastq outputs --- modules/nf-core/cellranger/mkfastq/main.nf | 2 +- modules/nf-core/cellrangerarc/mkfastq/main.nf | 2 +- modules/nf-core/cellrangeratac/mkfastq/main.nf | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/cellranger/mkfastq/main.nf b/modules/nf-core/cellranger/mkfastq/main.nf index ab03f984572..67f08fc2479 100644 --- a/modules/nf-core/cellranger/mkfastq/main.nf +++ b/modules/nf-core/cellranger/mkfastq/main.nf @@ -8,7 +8,7 @@ process CELLRANGER_MKFASTQ { tuple val(meta), path(csv), path(bcl) output: - tuple val(meta), path("*_outs/outs/fastq_path/*.fastq.gz"), emit: fastq + tuple val(meta), path("*_outs/outs/fastq_path/{*.fastq.gz,**/*.fastq.gz}"), emit: fastq tuple val(meta), path("*_outs/outs/fastq_path/Reports") , emit: reports tuple val(meta), path("*_outs/outs/fastq_path/Stats") , emit: stats tuple val(meta), path("*_outs/outs/interop_path/*.bin") , emit: interop diff --git a/modules/nf-core/cellrangerarc/mkfastq/main.nf b/modules/nf-core/cellrangerarc/mkfastq/main.nf index d8ec92f7917..ff3c123ebc9 100644 --- a/modules/nf-core/cellrangerarc/mkfastq/main.nf +++ b/modules/nf-core/cellrangerarc/mkfastq/main.nf @@ -14,7 +14,7 @@ process CELLRANGERARC_MKFASTQ { output: path "versions.yml", emit: versions - path "${bcl.getSimpleName()}/outs/fastq_path/*.fastq.gz" , emit: fastq + path "${bcl.getSimpleName()}/outs/fastq_path/{*.fastq.gz,**/*.fastq.gz}" , emit: fastq when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/cellrangeratac/mkfastq/main.nf b/modules/nf-core/cellrangeratac/mkfastq/main.nf index f5856ad4c28..3c00c25e926 100644 --- a/modules/nf-core/cellrangeratac/mkfastq/main.nf +++ b/modules/nf-core/cellrangeratac/mkfastq/main.nf @@ -15,7 +15,7 @@ process CELLRANGERATAC_MKFASTQ { output: path "versions.yml", emit: versions - path "${bcl.getSimpleName()}/outs/fastq_path/*.fastq.gz" , emit: fastq + path "${bcl.getSimpleName()}/outs/fastq_path/{*.fastq.gz,**/*.fastq.gz}" , emit: fastq when: task.ext.when == null || task.ext.when