change oras with https for singularity #111
Conversation
|
There was a problem hiding this comment.
Thanks for fixing this, there's another local module modules/local/vcf_to_csv/main.nf that also uses oras://. Could this be changed as well?
| @@ -4,7 +4,7 @@ process VARIANT_EXTRACTOR { | |||
|
|
|||
| conda "${moduleDir}/environment.yml" | |||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | |||
| 'oras://community.wave.seqera.io/library/htslib_pysam_tabix_pip_variant-extractor:a12ef217eccf6ba8': | |||
| 'https://community.wave.seqera.io/library/htslib_pysam_tabix_pip_variant-extractor:a12ef217eccf6ba8': | |||
There was a problem hiding this comment.
I don't think this is the correct adress.
singularity pull https://community.wave.seqera.io/library/htslib_pysam_tabix_pip_variant-extractor:a12ef217eccf6ba8
WARNING: Authentication token file not found : Only pulls of public images will succeed
FATAL: The requested image was not found in the library
There was a problem hiding this comment.
Then, I think it is not possible to convert oras to https for wave containers. I have been checking https://seqera.io/containers/
and found out this.
Do you have another idea to create mulled images other than seqera containers?
There was a problem hiding this comment.
You should be able to check a HTTPS box when building.
There was a problem hiding this comment.
There was a problem hiding this comment.
thanks for the link! new singularity images are working for me now. Can you please review it again? Thanks
tests/.nftignore
Outdated
There was a problem hiding this comment.
conflicting with my previous merge.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).