You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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?
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
nf-core version 2.7.2
HPC
Local executor
Redhat Linux 7.9
this module has nested double quotes instead of internal single quotes - is it terminating early?
Yes you are right @rdwngs, the module is updated now in the dev branch and the image can be downloaded for running the dev branch. Thanks for reporting!
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 nextflow inspect that does resolve the container correctly, but it will take a while until the whole codebase of nf-core download has been rewritten to use the outputs of inspect (Certainly not for version 2.10, possibly also not yet 2.11). Thus, I suppose, the next pipeline release will happen earlier.
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
The text was updated successfully, but these errors were encountered: