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Minor corrections in README file - #94

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jfy133 merged 38 commits into
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Feb 16, 2026
Merged

Minor corrections in README file#94
jfy133 merged 38 commits into
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@MeriamOs

@MeriamOs MeriamOs commented Feb 5, 2026 •
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PR checklist

Updated README file to correct nextflow version batch and add extra information on running the pipeline offline or on HPC.

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • README.md is updated (including new tool citations and authors/contributors).

Note:
The "nf-core pipelines download nf-core/coproid" fails because it uses nextflow 25.10.3. The documentation has been updated to use nextflow ≤ 24.10.5.

@nf-core-bot

nf-core-bot commented Feb 5, 2026

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.0.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions Bot commented Feb 5, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1c63bc8

+| ✅ 226 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   5 tests had warnings |!
Details

❗ Test warnings:

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: docs/images/nf-core-coproid_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-coproid_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-02-15 22:50:56

@MeriamOs MeriamOs mentioned this pull request Feb 5, 2026
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@MeriamOs

MeriamOs commented Feb 5, 2026

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The "nf-core pipelines download nf-core/coproid" fails because it uses nextflow 25.10.3. The documentation has been updated to use nextflow ≤ 24.10.5.

jfy133
jfy133 reviewed Feb 6, 2026
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Even though it's a tiny patch release, you're missing a CHANGELOG update!

@jfy133

jfy133 commented Feb 6, 2026

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The "nf-core pipelines download nf-core/coproid" fails because it uses nextflow 25.10.3. The documentation has been updated to use nextflow ≤ 24.10.5.

Also @MeriamOs this should be resolved if you merge in the latest templates I would imagine.

It would make a lot of sense to include this in the patch release rather than having a restrictive maximum NXF verison.

@MeriamOs

MeriamOs commented Feb 6, 2026 •
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@jfy133 oops! Thanks for pointing that out!
Added now here: #97

Even though it's a tiny patch release, you're missing a CHANGELOG update!

@MeriamOs

MeriamOs commented Feb 6, 2026

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And @jfy133 I'm planning to do this in the not so near future, but trying to get a paper out for JOSS.

Manuscript is all ready to go just needed to get these reviewers comments incorporated, so have prioritised these changes.
openjournals/joss-reviews#9324 (comment)

Aiming to get the new templates incorporated into the next patch release!

The "nf-core pipelines download nf-core/coproid" fails because it uses nextflow 25.10.3. The documentation has been updated to use nextflow ≤ 24.10.5.

Also @MeriamOs this should be resolved if you merge in the latest templates I would imagine.

It would make a lot of sense to include this in the patch release rather than having a restrictive maximum NXF verison.

@jonasscheid

jonasscheid commented Feb 10, 2026

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If it's published, make sure you mention it on the nf-core website :)

@jfy133

jfy133 commented Feb 11, 2026

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@MeriamOs #89

I've done the template merge there! Please look at it thoroughly (and maybe test a bit), but I think I transferred the pipeline specific things correctly!

@jfy133

jfy133 commented Feb 11, 2026

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And merging that in should update this PR too

johnvusich
johnvusich approved these changes Feb 11, 2026
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Happy to review the new template in the next patch release as well

@MeriamOs
Merge pull request #89 from nf-core/nf-core-template-merge-3.5.1
1c63bc8 
Important! Template update for nf-core/tools v3.5.1
@MeriamOs

MeriamOs commented Feb 16, 2026 •
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@johnvusich new template has been merged by the amazing @jfy133 and seems to have fixed the error described by you in #87 !

The only test that doesn't run to completion is the nf-test / conda with Nextflow version 25.04.0. Singularity and docker work with 25.04.0, and all work with the newest Nextflow. @johnvusich and @jfy133 is this still okay to merge?

Happy to review the new template in the next patch release as well

@jfy133
jfy133 self-requested a review February 16, 2026 17:47
jfy133
jfy133 approved these changes Feb 16, 2026
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Ok, so I'm going to give this a ✅ for the purposes of getting this out for the paper, however:

  1. None of the Conda tests are working actually (if you look inside the test logs it fails elsewhere, you have to look at the summary page to see the true results, long story but we are stuck with some GHA restrictions)

  2. However, Conda support is only a (strong) recommendation not a requirement for nf-core (https://nf-co.re/docs/guidelines/pipelines/recommendations/bioconda)

  3. The Conda issues are actually upstream problems with the Conda recipes not the pipeline itself (so would take longer to fix)

  4. I also noted during my review that there is a lot of strict syntax violations and other suboptimal code that will be possible become more problematic in the future.

However given the the pipeline works with the current versions when using docker/Singularity (which is mandatory requirement) I'll allow this to merged and the release cut on the proviso that Conda and strict syntax fixes are made into issues and will be worked on in the future with high priority!

@MeriamOs please finish ALL steps of the release here: https://nf-co.re/docs/checklists/pipeline_release

And a note to the paper reviewers (on behalf of the nf-core core team), we don't like to be too restrictive with nextflow version pinning (i.e. setting a max version) as generally Nextflow Is pretty good with backwards compatibility and we don't want to see too much variation across all the pipelines in the community, which is why this pipeline only has a minimum version (which we have just bumped in the previous PR)

@jfy133
jfy133 merged commit 045d569 into master Feb 16, 2026
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@johnvusich johnvusich johnvusich approved these changes
@maxibor maxibor Awaiting requested review from maxibor

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@MeriamOs @nf-core-bot @jfy133 @jonasscheid @johnvusich