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Merging template updates 2.11 #683

Merged
merged 7 commits into from
Dec 20, 2023
Merged

Merging template updates 2.11 #683

merged 7 commits into from
Dec 20, 2023

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d4straub
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@d4straub d4straub commented Dec 20, 2023 •
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This is for template update 2.11

As of the time of creating this PR there seems to be no conda package for that nf-core/tools version available yet so I cannot lint locally yet (i.e. stuff might go wrong).

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/ampliseq 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>).
  • 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 Dec 20, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9742624

+| ✅ 158 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.11
  • Run at 2023-12-20 13:46:45

@d4straub
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d4straub commented Dec 20, 2023 •
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Current fails have two reasons:
(1) docker.io/biocontainers/biocontainers:v1.2.0_cv1 / https://www.docker.com/biocontainers/biocontainers:v1.2.0_cv1 isnt working with docker, singularity works though. That lets all tests fail that format reference taxonomy databases.
(2) .test.snap doesnt match for test_reftaxcustom, test_qiimecustom, test_doubleprimers, test_novaseq: MultiQC version update changes multiQC md5sums, also CUSTOM_DUMPSOFTWAREVERSIONS version string changed with module update.

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d4straub commented Dec 20, 2023 •
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Ok, so the remaining issue in all failing tests is

    Digest: sha256:3332df09060b4336e26929bb505a598d36137ad46eeb331dcb8846ca5776ca6c
    Status: Downloaded newer image for biocontainers/biocontainers:v1.2.0_cv1
    touch: cannot touch '.command.trace': Permission denied

for modules

NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY
NFCORE_AMPLISEQ:AMPLISEQ:SINTAX_TAXONOMY_WF:FORMAT_TAXONOMY_SINTAX
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME

I assume the changes in nextflow.config produce the error, the entry docker.userEmulation = true was removed and runOptions = '-u $(id -u):$(id -g)' was added. Will need to test.

Container biocontainers/biocontainers:v1.2.0_cv1 was changed from 2.3.2 to 2.4.0 to 'ubuntu:20.04'. But biocontainers/biocontainers:v1.2.0_cv1 was needed, see #502 (comment), so the change was reverted back to biocontainers/biocontainers:v1.2.0_cv1 in #503. The issue was that a container is needed that contains tar, unzip, and gunzip (which isnt true for the ubuntu container).

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d4straub commented Dec 20, 2023 •
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Container issue related to nf-core/tools#2607

maxulysse
maxulysse approved these changes Dec 20, 2023
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LGTM

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Thanks!

@d4straub d4straub merged commit 4b616ed into nf-core:dev Dec 20, 2023
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@d4straub d4straub deleted the merging-template-updates-2-11 branch December 20, 2023 14:11
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