Unverified Commit 89a1af53 authored by Chris Cheshire's avatar Chris Cheshire Committed by GitHub
Browse files

Merge pull request #128 from drpatelh/ubuntu 

Replace gawk containers with ubuntu
parents 5165e836 c48d5472

modules/local/export_meta.nf

+3 −3
Original line number Diff line number Diff line 
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

modules/local/linux/awk.nf

+3 −3
Original line number Diff line number Diff line
@@ -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)

modules/local/linux/awk_script.nf

+3 −3
Original line number Diff line number Diff line
@@ -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)

modules/local/linux/cut.nf

+3 −3
Original line number Diff line number Diff line
@@ -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)

modules/local/linux/sort.nf

+3 −3
Original line number Diff line number Diff line
@@ -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)

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