From 69c6081efe8c780032a27b4b26b758b5bddb5129 Mon Sep 17 00:00:00 2001 From: Anne Marie Noronha Date: Mon, 20 Nov 2023 19:41:10 -0500 Subject: [PATCH] fix docker registry issues --- modules/local/agfusion/batch/main.nf | 4 ++-- modules/local/agfusion/download/main.nf | 4 ++-- modules/local/metafusion/main.nf | 4 ++-- modules/local/oncokb/fusionannotator/main.nf | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/modules/local/agfusion/batch/main.nf b/modules/local/agfusion/batch/main.nf index 95f3fa2..0544b5d 100644 --- a/modules/local/agfusion/batch/main.nf +++ b/modules/local/agfusion/batch/main.nf @@ -5,8 +5,8 @@ process AGFUSION_BATCH { // Note: 2.7X indices incompatible with AWS iGenomes. conda 'bioconda::agfusion=1.252' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'cmopipeline/agfusion:0.0.6' : - 'cmopipeline/agfusion:0.0.6' }" + 'docker://cmopipeline/agfusion:0.0.6' : + 'docker://cmopipeline/agfusion:0.0.6' }" input: tuple val(meta), path(fusions) diff --git a/modules/local/agfusion/download/main.nf b/modules/local/agfusion/download/main.nf index ad76dac..6647777 100644 --- a/modules/local/agfusion/download/main.nf +++ b/modules/local/agfusion/download/main.nf @@ -4,8 +4,8 @@ process AGFUSION_DOWNLOAD { // Note: 2.7X indices incompatible with AWS iGenomes. conda 'bioconda::agfusion=1.252' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'cmopipeline/agfusion:0.0.6' : - 'cmopipeline/agfusion:0.0.6' }" + 'docker://cmopipeline/agfusion:0.0.6' : + 'docker://cmopipeline/agfusion:0.0.6' }" input: val(ensembl_release) diff --git a/modules/local/metafusion/main.nf b/modules/local/metafusion/main.nf index e3e8120..40b90ee 100644 --- a/modules/local/metafusion/main.nf +++ b/modules/local/metafusion/main.nf @@ -3,8 +3,8 @@ process METAFUSION { label "process_low" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'cmopipeline/metafusion:0.0.6' : - 'cmopipeline/metafusion:0.0.6' }" + 'docker://cmopipeline/metafusion:0.0.6' : + 'docker://cmopipeline/metafusion:0.0.6' }" input: tuple val(meta), path(cff) diff --git a/modules/local/oncokb/fusionannotator/main.nf b/modules/local/oncokb/fusionannotator/main.nf index 1a263c5..bd311e7 100644 --- a/modules/local/oncokb/fusionannotator/main.nf +++ b/modules/local/oncokb/fusionannotator/main.nf @@ -5,8 +5,8 @@ process ONCOKB_FUSIONANNOTATOR { // Note: 2.7X indices incompatible with AWS iGenomes. //conda "shahcompbio::oncokb-annotator=2.3.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'cmopipeline/oncokb-annotator:0.0.1' : - 'cmopipeline/oncokb-annotator:0.0.1' }" + 'docker://cmopipeline/oncokb-annotator:0.0.1' : + 'docker://cmopipeline/oncokb-annotator:0.0.1' }" input: tuple val(meta), path(cff)