From 1b6cd4c282932c2b059dc0cc123f4de057f6b49a Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Thu, 9 Dec 2021 09:14:44 +0100 Subject: [PATCH 1/2] bump version --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 56197ec..9fdfbba 100644 --- a/nextflow.config +++ b/nextflow.config @@ -46,7 +46,7 @@ process.shell = ['/bin/bash', '-euo', 'pipefail'] cleanup = true -VERSION = '1.7.1' +VERSION = '1.7.2' DOI = 'https://zenodo.org/badge/latestdoi/358400957' manifest { From b7db808686042a84e6f6c0e207f2acbb8cfe05b3 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Thu, 9 Dec 2021 10:02:54 +0100 Subject: [PATCH 2/2] add R dependency to Picard metrics --- modules/03_metrics.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/03_metrics.nf b/modules/03_metrics.nf index 839f047..fe8ff12 100644 --- a/modules/03_metrics.nf +++ b/modules/03_metrics.nf @@ -52,7 +52,8 @@ process METRICS { tag "${name}" publishDir "${params.output}/${name}/metrics/gatk_multiple_metrics", mode: "copy" - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + // NOTE: the method CollectMultipleMetrics has a hidden dependency to R for making plots + conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0 r::r=3.6.0" : null) input: tuple val(name), val(type), file(bam), file(bai)