From 6ae267c249e89cf93ae4620a42d92d5f31856d4b Mon Sep 17 00:00:00 2001 From: Joris van Steenbrugge Date: Fri, 13 Sep 2024 11:18:34 +0200 Subject: [PATCH 1/2] Update container image to include RTGtools --- modules/nf-core/happy/happy/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/happy/happy/main.nf b/modules/nf-core/happy/happy/main.nf index b3cc12d5d71..a272fd36f9f 100644 --- a/modules/nf-core/happy/happy/main.nf +++ b/modules/nf-core/happy/happy/main.nf @@ -5,8 +5,8 @@ process HAPPY_HAPPY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/hap.py:0.3.14--py27h5c5a3ab_0': - 'biocontainers/hap.py:0.3.14--py27h5c5a3ab_0' }" + 'oras://community.wave.seqera.io/library/hap.py_rtg-tools:020cb72d1cbfac7a': + 'community.wave.seqera.io/library/hap.py_rtg-tools:2ebb433f3ce976d3' }" input: tuple val(meta), path(query_vcf), path(truth_vcf), path(regions_bed), path(targets_bed) From fa3ed5bbd73e857bfaacf8f382387bb62db86d0c Mon Sep 17 00:00:00 2001 From: Joris van Steenbrugge Date: Fri, 27 Sep 2024 13:26:17 +0200 Subject: [PATCH 2/2] add happy-python to dependencies --- modules/nf-core/rtgtools/vcfeval/environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/nf-core/rtgtools/vcfeval/environment.yml b/modules/nf-core/rtgtools/vcfeval/environment.yml index 8aa83cdc41d..038fc3ccd69 100644 --- a/modules/nf-core/rtgtools/vcfeval/environment.yml +++ b/modules/nf-core/rtgtools/vcfeval/environment.yml @@ -3,3 +3,4 @@ channels: - bioconda dependencies: - bioconda::rtg-tools=3.12.1 + - bioconda::happy-python=0.2.1rc0