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nf-core download skips 'bowtie2 align' singularity image with container string parsing error #318
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I am having the exact same problem with chipseq version 2.0.0 and nf-core download, and was wondering if there were any updates; very similar system information as in the original report, but here are my details: nextflow version 22.10.4.5836 |
Yes you are right @rdwngs, the module is updated now in the |
Sadly, downloading exactly this pipeline version that contains the affected module will not be possible to support with the current nf-core download, for reasons explained here. Nextflow has received a new functionality |
Fixed in #339 |
Description of the bug
When attempting to download and install chipseq-2.0.0 with singularity containers, the 'bowtie2 align' image gives a container string parsing error. I noticed the container string in main.nf for this module has nested double quotes instead of internal single quotes - is it terminating early?
container "${ workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ?
"https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" :
"quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" }"
Command used and terminal output
Relevant files
https://github.com/nf-core/chipseq/blob/master/modules/nf-core/modules/bowtie2/align/main.nf
System information
nextflow version 22.10.0.5826
nf-core version 2.6
HPC
Local executor
Singularity container engine
Redhat Linux 8.5
chipseq version 2.0.0
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