Edit multiQC report#53
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KateSakharova merged 42 commits intodevfrom May 6, 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: 3.5.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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vagkaratzas
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Minor things to remove and looks good so far! Let's wait for new nf-core tools patch updates for the next ones
| > As all assemblies in ENA are submitted as ‘analyses’, for each assembly submission, Webin will report a unique accession number that starts with ERZ. | ||
| > For most assemblies, this accession number is for **internal processing only** and will not be visible in the browser. | ||
| > As a result, for most assemblies you will receive additional post-processing accession numbers starting with GCA\_. | ||
| > More information about accessions can be found in ENA docs: https://ena-docs.readthedocs.io/en/latest/submit/assembly.html#accessions.' |
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| > More information about accessions can be found in ENA docs: https://ena-docs.readthedocs.io/en/latest/submit/assembly.html#accessions.' | |
| > More information about accessions can be found in ENA docs: https://ena-docs.readthedocs.io/en/latest/submit/assembly.html#accessions. |
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I think this should be in the MAGs/bins section
And specify that it's for MAGs only.
Because it's something that we know for sure.
I know that ERZs for bins and primary metagenomes ARE displayed on the portal and they are used to reference the data forever. Docs state the opposite, but I would ask ENA before assume that it's true for ALL assemblies :/
ochkalova
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Apr 29, 2026
| > As all assemblies in ENA are submitted as ‘analyses’, for each assembly submission, Webin will report a unique accession number that starts with ERZ. | ||
| > For most assemblies, this accession number is for **internal processing only** and will not be visible in the browser. | ||
| > As a result, for most assemblies you will receive additional post-processing accession numbers starting with GCA\_. | ||
| > More information about accessions can be found in ENA docs: https://ena-docs.readthedocs.io/en/latest/submit/assembly.html#accessions.' |
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I think this should be in the MAGs/bins section
And specify that it's for MAGs only.
Because it's something that we know for sure.
I know that ERZs for bins and primary metagenomes ARE displayed on the portal and they are used to reference the data forever. Docs state the opposite, but I would ask ENA before assume that it's true for ALL assemblies :/
ochkalova
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Apr 30, 2026
mberacochea
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Apr 30, 2026
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| def topic_versions_string = topic_versions.versions_tuple | ||
| .map { process, tool, version -> | ||
| [ process[process.lastIndexOf(':')+1..-1], " ${tool}: ${version}" ] | ||
| } | ||
| .groupTuple(by:0) | ||
| .map { process, tool_versions -> | ||
| tool_versions.unique().sort() | ||
| "${process}:\n${tool_versions.join('\n')}" | ||
| } |
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I know this is nf-core stuff, but this code is awful... this should be buried in a lib somewhere
mberacochea
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Apr 30, 2026
mberacochea
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Apr 30, 2026
mberacochea
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Apr 30, 2026
mberacochea
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Apr 30, 2026
mberacochea
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Apr 30, 2026
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Left some tiny comments 🥇
| conda "${moduleDir}/environment.yml" | ||
| // TODO: version is temporarily set to 1.25.1 to avoid segfault happening in 1.32 | ||
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| // Container was taken from linux/arm64 instead of linux/amd64 |
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What does this mean?
Can you just update to the latest version in nf-core?
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I think their default containers are from linux/amd64
the latest gave me seqfault
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That is some aggresive circling hahah (I can almost see your face while doing that).
OK, I this may cause issues in linux machines then.. if this breaks I'll try to help
| // Uncomment function in methodsDescriptionText to render in MultiQC report | ||
| def reference_text = [ | ||
| "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>" | ||
| '<li>Richardson, L., Allen, B., Baldi, G., Beracochea, M., Bileschi, M. L., Burdett, T., ... & Finn, R. D. (2023). MGnify: the microbiome sequence data analysis resource in 2023. Nucleic acids research, 51(D1), D753-D759. doi: <a href="https://doi.org/10.1093/nar/gkac1080">10.1093/nar/gkac1080</a></li>', |
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I have a script to help with these - https://gist.github.com/mberacochea/50ba897865f53767a762e240a405f6c4
just for future ref :)
mberacochea
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Thanks @KateSakharova!
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Fixing Create citations functions required by template #49
add final reports with metadata, samples and ERZs into multiqc.html
Fixing [ENA] For metagenomic assemblies the pipeline should inform users that ERZ accessions are just temporary #25 by adding note to README and info to muliqc report
some minor fixes
I have changed container ena-webin+newer toolkit and it seems resolved Include webin-cli jar into container, remove ENA_WEBIN_CLI_DOWNLOAD module #50
Resolved annoying Update pipeline to use MultiQC of latest version #46 issue with creating seqera containers image with linux/arm64 instead of linux/amd64 🤦♀️
TODO: update genome_uploader after EBI-Metagenomics/genome_uploader#49 because header is required for multiqc
TODO: fix snapshots after all previous TODOs are done