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Replace vanilla Linux Biocontainer with Ubuntu (#1557)

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Harshil Patel 2022-04-22 14:50:07 +01:00 committed by GitHub
parent c17d1a7a7b
commit 9aadd9a6d3
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3 changed files with 7 additions and 7 deletions
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4
modules/cat/fastq/main.nf
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@ -4,8 +4,8 @@ process CAT_FASTQ {
conda (params.enable_conda ? "conda-forge::sed=4.7" : null) conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ 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' : 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'biocontainers/biocontainers:v1.2.0_cv1' }" 'ubuntu:20.04' }"
input: input:
tuple val(meta), path(reads, stageAs: "input*/*") tuple val(meta), path(reads, stageAs: "input*/*")

4
modules/gunzip/main.nf
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@ -4,8 +4,8 @@ process GUNZIP {
conda (params.enable_conda ? "conda-forge::sed=4.7" : null) conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ 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' : 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'biocontainers/biocontainers:v1.2.0_cv1' }" 'ubuntu:20.04' }"
input: input:
tuple val(meta), path(archive) tuple val(meta), path(archive)

6
modules/untar/main.nf
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@ -2,10 +2,10 @@ process UNTAR {
tag "$archive" tag "$archive"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "conda-forge::tar=1.34" : null) conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' : 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'biocontainers/biocontainers:v1.2.0_cv2' }" 'ubuntu:20.04' }"
input: input:
tuple val(meta), path(archive) tuple val(meta), path(archive)