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Merging template updates #71

Merged
merged 13 commits into from
Jun 12, 2024
Merged

Merging template updates #71

merged 13 commits into from
Jun 12, 2024

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kbestak
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@kbestak kbestak commented Jun 11, 2024

This is a big one, template update 2.14 implemented, updated Mesmer, Cellpose, MultiQC, respective tests.
Dev is version-bumped to 1.1.0dev
Seqera container for MultiQC 1.22.1 to circumvent issue in gitpod - should this be only provided by the user?
#59
#62
#70

*** introduces bug that multiqc doesn't show custom qc results - neither with crops, nor quantifictions - should be fixed ASAP, but this PR is giant already.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/molkart branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Jun 11, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3a408e9

+| ✅ 211 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-12 09:19:36

@FloWuenne FloWuenne self-assigned this Jun 11, 2024
FloWuenne
FloWuenne reviewed Jun 11, 2024
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modules/nf-core/cellpose/meta.yml Outdated
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Nice correction of my name there 😉 !

modules/nf-core/multiqc/main.nf
Comment on lines +6 to +7
'https://depot.galaxyproject.org/singularity/multiqc:1.22.2--pyhdfd78af_0' :
'biocontainers/multiqc:1.22.2--pyhdfd78af_0' }"
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@FloWuenne FloWuenne Jun 11, 2024 •
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You mention Seqera containers in the PR description for MultiQC. If you wanted to use Seqera wave containers here, you could use the following. Up to you which one to go with for the moment. I have tested the docker container below and that worked.

Suggested change
'https://depot.galaxyproject.org/singularity/multiqc:1.22.2--pyhdfd78af_0' :
'biocontainers/multiqc:1.22.2--pyhdfd78af_0' }"
'oras://community.wave.seqera.io/library/pip_multiqc:dab7a0322e1851bb' :
'community.wave.seqera.io/library/pip_multiqc:2c2e276ad8997cc4' }"

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I updated it in the module config as changing the main.nf from MultiQC would cause a failure with linting. I would prefer to do it here if possible, but it would anyways only be to circumvent the multiqc gitpod issue.

This was linked to issues Jun 11, 2024
nf-core/molkart template update 2.14.1 #70
Closed
Deepcell_mesmer doesn't work on AWS with WAVE and FUSION #56
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@FloWuenne
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One additional comment. Singularity tests failed for me after the template update.
nextflow run . -profile test,singularity --outdir ./test

The error message I received was:

ERROR ~ Error executing process > 'NFCORE_MOLKART:MOLKART:MINDAGAP_DUPLICATEFINDER (mem_only)'

Caused by:
  Process `NFCORE_MOLKART:MOLKART:MINDAGAP_DUPLICATEFINDER (mem_only)` terminated with an error exit status (255)


Command executed:

  duplicate_finder.py \
      spots.txt \
      90
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_MOLKART:MOLKART:MINDAGAP_DUPLICATEFINDER":
      mindagap: $(mindagap.py test -v)
  END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  FATAL:   container creation failed: image driver mount failure: image driver squashfuse_ll instance exited with error: squashfuse_ll exited: fuse: failed to open /dev/fuse: Operation not permitted

Can you check on your end whether it works on HPC @kbestak ?

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kbestak commented Jun 12, 2024

To address the Mindagap Singularity issue:

  • For me it worked both in Gitpod, and on our HPC for the latest Nextflow version (24.04.2.5914)
  • I've attempted to add singularity tests into the CI to make sure the test profile also runs with Singularity, but I got a singularity not found error in the runners so I've again removed it.

@kbestak kbestak merged commit a28da2c into nf-core:dev Jun 12, 2024
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@kbestak kbestak deleted the merging-template-updates branch June 12, 2024 12:00
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@FloWuenne FloWuenne FloWuenne approved these changes

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nf-core/molkart template update 2.14.1 Deepcell_mesmer doesn't work on AWS with WAVE and FUSION
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