From 89e5473b4493320a4842ce0dca4897a6c3f8b77a Mon Sep 17 00:00:00 2001 From: Sruthi Suresh Date: Thu, 12 Nov 2020 19:07:44 -0600 Subject: [PATCH] Updated modules with the changed container format --- software/bedtools/complement/main.nf | 8 ++------ software/bedtools/slop/main.nf | 9 +++------ 2 files changed, 5 insertions(+), 12 deletions(-) diff --git a/software/bedtools/complement/main.nf b/software/bedtools/complement/main.nf index 8ca54a39..402557c1 100644 --- a/software/bedtools/complement/main.nf +++ b/software/bedtools/complement/main.nf @@ -10,12 +10,8 @@ process BEDTOOLS_COMPLEMENT { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0 " - } else { - container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0" - } + conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null) + container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0" input: tuple val(meta), path(beds) diff --git a/software/bedtools/slop/main.nf b/software/bedtools/slop/main.nf index a4d282be..e43c9086 100644 --- a/software/bedtools/slop/main.nf +++ b/software/bedtools/slop/main.nf @@ -10,12 +10,9 @@ process BEDTOOLS_SLOP { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0 " - } else { - container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0" - } + conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null) + container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0" + input: tuple val(meta), path(beds)