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added metaT support to assembly flow - #106
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KateSakharova
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❌ nf-test failed with latest Nextflow versionNote Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
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`GENOMESUBMIT` decides whether to (re)compute completeness and contamination
with CheckM2 using a truthiness test:
genome_evaluation_input: !(meta.completeness) || !(meta.contamination) || !(meta.stats_generation_software)
In Groovy `0` is falsey, so a genome with a legitimate value of 0 -- a clean MAG
with 0% contamination, or a highly incomplete one with 0% completeness -- is
misread as "no stats provided" and is sent to `GENOME_EVALUATION`.
For a samplesheet that supplies stats for every row this silently re-computes
part of the run (including downloading the CheckM2 database) and then overrides
the supplied values, and it sets `stats_generation_software` from the tool name
reported by the module. The result is an inconsistent metadata column across the
submission: the affected rows end up with a recomputed version string while the
remaining rows keep the one from the samplesheet.
Test for absence instead of falsiness, matching the idiom already used elsewhere
in the same workflow (e.g. `meta.RNA_presence == null` for the RNA branch).
Verification with an nf-schema 2.5.1 probe over a three-row samplesheet (the
same `samplesheetToList` call the pipeline makes):
* a samplesheet value of `0.0` arrives as a `java.math.BigDecimal` 0, so the
old predicate routes that row to `GENOME_EVALUATION` and the new one does
not;
* an *empty* field arrives as `null`, so rows with genuinely missing
statistics still take the `GENOME_EVALUATION` branch with the new
predicate.
The `genome_coverage` branch (`COVERM_GENOME`) is intentionally left alone: its
schema field declares `exclusiveMinimum: 0`, so `0` is rejected at samplesheet
validation, while an omitted value arrives as `null` and both predicates then
agree.
…sing Fix zero completeness/contamination being treated as missing
Vkale1
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Oct 16, 2026
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Hey! Lovely :) couple very unimportant small things.
Update the metagenomic assemblies section of the README
Assembly_metadata section of the multi-qc config would also have library now?
Same for generate_assembly_manifest meta.yml for completeness
The generate assembly manifest snapshot still has the old snapshot with previous uploader version also.. is this normal to keep?
ochkalova
approved these changes
Oct 19, 2026
Comment on lines
+95
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| }, | ||
| "library_strategy": { | ||
| "type": "string", | ||
| "enum": ["metagenome", "metatranscriptome"], | ||
| "errorMessage": "Assembly library strategy should be metagenome or metatranscriptome", | ||
| "description": "Assembly library strategy: metagenome or metatranscriptome. Default: metagenome", | ||
| "default": "metagenome", | ||
| "meta": ["library_strategy"] |
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The mode name "metagenomic_assembly" becomes a bit confusing with this change 🤔
Maybe we will have to rename it? But I don't see any good options :sad:
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or just assembly
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Let's leave it like this until somebody will raise it
It's fine 🥴
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Resolving #100 and #114
library_strategyto assembly input samplesheet. Default value:metagenome