From c48d54725c6def08ed21adb50e6e7388ac97ed6f Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 27 May 2022 10:08:57 +0100 Subject: [PATCH] Replace gawk containers with ubuntu --- modules/local/export_meta.nf | 6 +++--- modules/local/linux/awk.nf | 6 +++--- modules/local/linux/awk_script.nf | 6 +++--- modules/local/linux/cut.nf | 6 +++--- modules/local/linux/sort.nf | 6 +++--- 5 files changed, 15 insertions(+), 15 deletions(-) diff --git a/modules/local/export_meta.nf b/modules/local/export_meta.nf index ca6b98c0..6a18e362 100644 --- a/modules/local/export_meta.nf +++ b/modules/local/export_meta.nf @@ -1,10 +1,10 @@ process EXPORT_META { label 'process_min' - conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null) + conda (params.enable_conda ? "conda-forge::sed=4.7" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gawk:5.1.0' : - 'quay.io/biocontainers/gawk:5.1.0' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'ubuntu:20.04' }" input: val meta diff --git a/modules/local/linux/awk.nf b/modules/local/linux/awk.nf index cad042d2..d56926f9 100644 --- a/modules/local/linux/awk.nf +++ b/modules/local/linux/awk.nf @@ -2,10 +2,10 @@ process AWK { tag "$meta.id" label 'process_ultralow' - conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null) + conda (params.enable_conda ? "conda-forge::sed=4.7" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' : - 'biocontainers/biocontainers:v1.2.0_cv1' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'ubuntu:20.04' }" input: tuple val(meta), path(input) diff --git a/modules/local/linux/awk_script.nf b/modules/local/linux/awk_script.nf index 18d42e1f..a9e4379b 100644 --- a/modules/local/linux/awk_script.nf +++ b/modules/local/linux/awk_script.nf @@ -2,10 +2,10 @@ process AWK_SCRIPT { tag "$meta.id" label 'process_min' - conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null) + conda (params.enable_conda ? "conda-forge::sed=4.7" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gawk:5.1.0' : - 'quay.io/biocontainers/gawk:5.1.0' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'ubuntu:20.04' }" input: tuple val(meta), path(input) diff --git a/modules/local/linux/cut.nf b/modules/local/linux/cut.nf index 090eb16d..088e6813 100644 --- a/modules/local/linux/cut.nf +++ b/modules/local/linux/cut.nf @@ -2,10 +2,10 @@ process CUT { tag "$meta.id" label 'process_min' - conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null) + conda (params.enable_conda ? "conda-forge::sed=4.7" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gawk:5.1.0' : - 'quay.io/biocontainers/gawk:5.1.0' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'ubuntu:20.04' }" input: tuple val(meta), path(input) diff --git a/modules/local/linux/sort.nf b/modules/local/linux/sort.nf index a7a684b8..9313d3dd 100644 --- a/modules/local/linux/sort.nf +++ b/modules/local/linux/sort.nf @@ -2,10 +2,10 @@ process SORT { tag "$meta.id" label 'process_ultralow' - conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null) + conda (params.enable_conda ? "conda-forge::sed=4.7" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gawk:5.1.0' : - 'quay.io/biocontainers/gawk:5.1.0' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'ubuntu:20.04' }" input: tuple val(meta), path(input)