Closed gq1 closed 3 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 5f50e79
+| ✅ 130 tests passed |+
#| ❔ 19 tests were ignored |#
!| ❗ 3 tests had warnings |!
Randomly we can see the following error message in the CI job when pulling docker image to singularity image. It will be OK if retrying. Different time it is on different image.
Failed to pull singularity image
command: singularity pull --name quay.io-sanger-tol-hifiasm_samtools-0.01.img.pulling.1717517205808 docker://quay.io/sanger-tol/hifiasm_samtools:0.01 > /dev/null
status : 255
message:
INFO: Converting OCI blobs to SIF format
INFO: Starting build...
Getting image source signatures
Copying blob sha256:03dae77ff45c4b21a524fe292d91a7[70](https://github.com/sanger-tol/genomeassembly/actions/runs/9370434094/job/25797382684#step:9:71)4d870b528d3e03c3624a4d48e7733d65
Copying blob sha256:efcc827fbbb39a149bce1b1b0951eccfa438d1d84153744033dd253856da8a08
Copying blob sha256:2ec3f7ad9b3ca7370ae62c6bdb36e3575239b5b0942163d36814c87efb3ff90d
Copying blob sha256:7[71](https://github.com/sanger-tol/genomeassembly/actions/runs/9370434094/job/25797382684#step:9:72)6ca30060043d1c1ba35c09e8eb2fda19788fc0d5ec491d85e866306207cc9
Copying blob sha256:8c61d418774c0c5a7be0036dd042add78077c4195d904abdba1080bad2539797
Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
Copying blob sha256:aab7f787139dee8557ebf54563c3e9e57c28d98e41e98f997c8af42c15b78b09
Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
Copying blob sha256:837d55536[72](https://github.com/sanger-tol/genomeassembly/actions/runs/9370434094/job/25797382684#step:9:73)0ebdfd52a582cc6333019e0cfe430ef7c24fb1[73](https://github.com/sanger-tol/genomeassembly/actions/runs/9370434094/job/25797382684#step:9:74)33f8d0fb9e7ec
Copying blob sha256:897362c12ca72fae6ca704[74](https://github.com/sanger-tol/genomeassembly/actions/runs/9370434094/job/25797382684#step:9:75)a9f2e9ced3a57c82f11f13033d4c3c73aae320a8
Copying blob sha256:3893cbe24e910b5f4aa84fde0aedaf93c0cd7fbd66a423c39cb1077d420[75](https://github.com/sanger-tol/genomeassembly/actions/runs/9370434094/job/25797382684#step:9:76)3e8
Copying blob sha256:d1b61e94977bd32162b9537fa73b2bde0c0e866044bf3b973c7a20501102e11d
Copying blob sha256:91e8b0e836771486163bed3d34cba2023210c2791b06d798bd2400afbda94c8d
Copying blob sha256:6a32[76](https://github.com/sanger-tol/genomeassembly/actions/runs/9370434094/job/25797382684#step:9:77)365367224313a0e554a59ca14ff290fbc4f9b5c773367d77a4be3d17e1
Copying config sha256:b660941f86fd8d23aeeef16b2cf9f3d1cc2472c4ad1f1659226aeaaed5d0fb67
Writing manifest to image destination
FATAL: While making image from oci registry: error fetching image to cache: while building SIF from layers: conveyor failed to get: while getting config
It seems this PR can fix the problem. I have tried several times. It also can fail but for different reasons.
If we merge this to the dev, probably @yumisims no need to use nf-core download
but we still need to found the problems from nf-core download if we need to use later.
Another solution for this error is to switch to use docker profile, and then we don't need to convert docker image to singularity image.
Another solution for this error is to switch to use docker profile, and then we don't need to convert docker image to singularity image.
Remind me why the singularity profile is currently used ?
Another solution for this error is to switch to use docker profile, and then we don't need to convert docker image to singularity image.
Remind me why the singularity profile is currently used ?
Use Singularity to run, less memory needed and thus it can run on the free Github runner, at least for TreeVal. For this pipeline, more disk space needed.
@ksenia-krasheninnikova
Can you have a look and we can merge to your dev
branch? And then you can pull the changes to your paper branch to make sure the CI can run.
Another question, can you exclude your paper directory to trigger the CI to run? There is no need to run the test if you just update the paper.
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).