From 4c811fde11383678d41d5eebd770395b303d9096 Mon Sep 17 00:00:00 2001 From: Justin Date: Sat, 6 Dec 2025 12:34:17 -0500 Subject: [PATCH 1/3] bump to ensembl-vep=113.4 and update containers --- modules/nf-core/vcf2maf/environment.yml | 2 +- modules/nf-core/vcf2maf/main.nf | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/vcf2maf/environment.yml b/modules/nf-core/vcf2maf/environment.yml index 4e617a0a11cc..2a656f4260eb 100644 --- a/modules/nf-core/vcf2maf/environment.yml +++ b/modules/nf-core/vcf2maf/environment.yml @@ -4,5 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ensembl-vep=113.3 + - bioconda::ensembl-vep=113.4 - bioconda::vcf2maf=1.6.22 diff --git a/modules/nf-core/vcf2maf/main.nf b/modules/nf-core/vcf2maf/main.nf index f964fc78315d..32cf68cbefe2 100644 --- a/modules/nf-core/vcf2maf/main.nf +++ b/modules/nf-core/vcf2maf/main.nf @@ -6,8 +6,8 @@ process VCF2MAF { // 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://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7c/7cbf9421f0bee23a93a35c5d0c7166ac1e89a40008d8e474cecfddb93226bf65/data': - 'community.wave.seqera.io/library/ensembl-vep_vcf2maf:2d40b60b4834af73' }" + 'oras://community.wave.seqera.io/library/ensembl-vep_vcf2maf:df9fb21816c1659e': + 'community.wave.seqera.io/library/ensembl-vep_vcf2maf:795c7ca795a6c63a' }" input: tuple val(meta), path(vcf) // Use an uncompressed VCF file! From 115d42dad956c3e07fcc611e174865412d433c8d Mon Sep 17 00:00:00 2001 From: Justin Date: Sat, 6 Dec 2025 13:13:53 -0500 Subject: [PATCH 2/3] added https:// to container links as required --- modules/nf-core/vcf2maf/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/vcf2maf/main.nf b/modules/nf-core/vcf2maf/main.nf index 32cf68cbefe2..fc7f1c8f9e5c 100644 --- a/modules/nf-core/vcf2maf/main.nf +++ b/modules/nf-core/vcf2maf/main.nf @@ -6,8 +6,8 @@ process VCF2MAF { // 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 ? - 'oras://community.wave.seqera.io/library/ensembl-vep_vcf2maf:df9fb21816c1659e': - 'community.wave.seqera.io/library/ensembl-vep_vcf2maf:795c7ca795a6c63a' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/04/04730c70a408fbee8c4a479832b340ca860113c09787061078a66ac56bd3ab56/data': + 'https://community.wave.seqera.io/library/ensembl-vep_vcf2maf:795c7ca795a6c63a' }" input: tuple val(meta), path(vcf) // Use an uncompressed VCF file! From 8eec2729c39839234e7757e8401aa6f9ef82d045 Mon Sep 17 00:00:00 2001 From: Justin Date: Sat, 6 Dec 2025 15:18:24 -0500 Subject: [PATCH 3/3] removed https:// from docker container. Misread the docs. --- modules/nf-core/vcf2maf/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/vcf2maf/main.nf b/modules/nf-core/vcf2maf/main.nf index fc7f1c8f9e5c..9ab5963e2310 100644 --- a/modules/nf-core/vcf2maf/main.nf +++ b/modules/nf-core/vcf2maf/main.nf @@ -7,7 +7,7 @@ process VCF2MAF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/04/04730c70a408fbee8c4a479832b340ca860113c09787061078a66ac56bd3ab56/data': - 'https://community.wave.seqera.io/library/ensembl-vep_vcf2maf:795c7ca795a6c63a' }" + 'community.wave.seqera.io/library/ensembl-vep_vcf2maf:795c7ca795a6c63a' }" input: tuple val(meta), path(vcf) // Use an uncompressed VCF file!