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Replace vanilla Linux Biocontainer with Ubuntu #1557

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merged 1 commit into from
Apr 22, 2022
Merged

Replace vanilla Linux Biocontainer with Ubuntu #1557

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4 changes: 2 additions & 2 deletions modules/cat/fastq/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process CAT_FASTQ {

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(reads, stageAs: "input*/*")
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4 changes: 2 additions & 2 deletions modules/gunzip/main.nf
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Expand Up @@ -4,8 +4,8 @@ process GUNZIP {

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(archive)
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6 changes: 3 additions & 3 deletions modules/untar/main.nf
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Expand Up @@ -2,10 +2,10 @@ process UNTAR {
tag "$archive"
label 'process_low'

conda (params.enable_conda ? "conda-forge::tar=1.34" : null)
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
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That's the only change that I don't get. Isn't it much more explicit to install tar in the untar module rather than sed which happens to include tar?

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Good spot! Missed that in the copy/paste. Wondering whether we need to care about this specifically because these tools should all be installed in the base Conda env anyway right? So do we go for standardisation here where we always define sed for modules using the ubuntu image or do we define the specific tools we are using? The latter could also be a pain in general because in most instances you will want to use multiple utilities like cat, awk, sed in the same module etc

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Fair point. If there's a way to pull in multiple standard tools that are also available in the container images, then that's probably preferable. Would that make available ps btw? I think that's needed for resource tracing, right?

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' :
'biocontainers/biocontainers:v1.2.0_cv2' }"
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"

input:
tuple val(meta), path(archive)
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