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nf-core download skips 'bowtie2 align' singularity image with container string parsing error #318

@rdwngs

Description

@rdwngs

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

nf-core download chipseq -c singularity

...
ERROR    Cannot parse container string in                                                                download.py:483
         'nf-core-chipseq-2.0.0/workflow/modules/nf-core/modules/bowtie2/align/main.nf':

             ${ workflow.containerEngine ==

         ⚠ Skipping this singularity image..

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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