Closed gq1 closed 9 months ago
main
branch :x:base
to dev
Hi @gq1,
It looks like this pull-request is has been made against the sanger-tol/variantcalling main
branch.
The main
branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main
are only allowed if they come from the sanger-tol/variantcalling dev
branch.
You do not need to close this PR, you can change the target branch to dev
by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.
Thanks again for your contribution!
nf-core lint
overall result: Passed :white_check_mark:Posted for pipeline commit fe45c30
+| ✅ 126 tests passed |+
#| ❔ 26 tests were ignored |#
@sanger-tolsoft fix linting
@nf-core-bot fix linting
@nf-core-bot fix linting
@nf-core-bot fix linting
The singularity tests are failing for deepvariant. This is not the case in modules repo, so it is some specific to our pipeline.
Pulling Singularity image docker://nf-core/deepvariant:1.5.0 [cache /lustre/scratch123/tol/teams/tolit/users/ps22/bin/singularity/nf-core-deepvariant-1.5.0.img]
ERROR ~ Error executing process > 'SANGERTOL_VARIANTCALLING:VARIANTCALLING:DEEPVARIANT_CALLER:DEEPVARIANT (3)'
Caused by:
Failed to pull singularity image
command: singularity pull --name nf-core-deepvariant-1.5.0.img.pulling.1695729700476 docker://nf-core/deepvariant:1.5.0 > /dev/null
status : 255
message:
FATAL: While making image from oci registry: error fetching image to cache: failed to get checksum for docker://nf-core/deepvariant:1.5.0: reading manifest 1.5.0 in docker.io/nf-core/deepvariant: errors:
denied: requested access to the resource is denied
unauthorized: authentication required
Manually pulling the image works with 6G memory not with 4G memory:
singularity pull --name nf-core-deepvariant-1.5.0.img.pulling.1695743033413 docker://quay.io/nf-core/deepvariant:1.5.0
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).