Release 2.1.0#149
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Co-authored-by: Florian De Temmerman <69114541+fbdtemme@users.noreply.github.com>
…d-denoise-step Feature/pna 1036 add denoise step
…me-and-metromap Update README and metromap
…ports Fix missing PNA report generation
…date-pixelator-to-0.21.4 Update pixelator to 0.21.4
Update metro map
Now that layout uses less memory we can also allocate less RAM and more CPUs to speed up the process.
switch layout process label to process_high
Bump version to 2.1.0
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It seems the failing pipeline download tests here are caused by this bug: nf-core/tools#3742 |
fbdtemme
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Sep 2, 2025
| and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). | ||
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| ## [[2.0.0](https://github.com/nf-core/pixelator/releases/tag/2.0.0)] - 2025-06-23 | ||
| ## [[2.1.0](https://github.com/nf-core/pixelator/releases/tag/x.x.x)] - YYYY-MM-DD |
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Reminder to update the date and version here
nvnieuwk
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Sep 16, 2025
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Some minor comments, but nothing blocking this release for me
| withName: PIXELATOR_PNA_LAYOUT { | ||
| ext.when = { !params.skip_layout } | ||
| ext.args = { | ||
| ext.when = { !params.skip_layout } |
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Try to limit the use of ext.when. This will get removed in the future in favor of if statements in the workflow itself. This is not a blocking issue for this release but it would be best to update this before the next release
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Yeah. We have a bunch of these, so I think it would make sense to go over all of them in one go.
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| """ | ||
| # Copy the full quarto dir from the read-only image into the workdir | ||
| cp -r /workspace/inst/quarto/ ./quarto/ |
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This seems like it should be a "reference" input to the module instead?
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We've been trying around with a bunch of different solutions to this - in the end this was the only one that actually worked. Why is a bit a of mystery to me.
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| # Hard coding the version for the stub, since for some | ||
| # reason it work in nf-test otherwise. | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| experiment-summary: 0.4.2 | ||
| END_VERSIONS | ||
| """ |
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This seems strange, the only difference between a stub run and a normal run is the difference in the bash code executed. What errors did you get here?
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Well, that is a good question. I could not replicate it now, so I have restored this to actually fetch the version as in the main script now.
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| {assert path(process.out.report_json.get(0).get(1)).exists()}, | ||
| {assert path(process.out.metadata.get(0).get(1)).exists()}, | ||
| {assert path(process.out.dataset.get(0).get(1)).exists()}, | ||
| {assert process.out.dataset.get(0).get(1).endsWith(".pxl")}, |
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This seems like a downgrade in test quality, is the output significantly different here?
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We have had a lot of issues with the tests being very brittle due to changing metadata. Since the pipeline basically only runs pixelator anytime we do an update of the pixelator version all the tests fail due to changes in the metadata of the files (that among other things contain the pixelator version run). As we have an extensive test suite on pixelator itself testing the content here has rather low return on investment for us, while causing a lot of extra work. In order to try to balance that out a bit we have decided to go for less stringent testing here. Does that make sense?
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Yes thank you, it does make sense. This might be worth to create an issue about and update the tests gradually in the future to ensure reproducibility of the pipeline
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| {assert path(process.out.report_json.get(0).get(1)).exists()}, | ||
| {assert path(process.out.metadata.get(0).get(1)).exists()}, |
…eports Simplify PNA_GENERATE_REPORTS subworkflow
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Release nf-core/pixelator 2.1.0.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).