Release v1.1.2#292
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…tagenome into bump-version-dev
Bump versions back to dev `1.1.2dev`
Introduce a new polishing parameter, cluster_with_reference, with a default value of true. This commit only adds the public parameter surface in nextflow.config and nextflow_schema.json. It does not change workflow behavior yet. The intent is to preserve the current default behavior while preparing a later commit that will make BLAST-based reference injection into clustering optional. Keeping the plumbing isolated makes the eventual PR easier to review and keeps this commit bisectable on its own.
Wire cluster_with_reference into FASTA_CONTIG_CLUST so BLAST can continue to run while the FASTA passed into clustering becomes configurable. When cluster_with_reference is true, keep the current behavior and cluster contigs together with BLAST-hit references. When it is false, still run BLAST and preserve its outputs, but use only the de novo contigs for clustering-related downstream steps. This commit is intentionally limited to the workflow behavior change. It does not update tests or documentation yet.
Add the minimum maintainer-friendly test coverage for cluster_with_reference=false. This commit should keep the focus on proving the feature contract rather than trying to validate full biological correctness. The goals are to preserve backward compatibility, verify that the new mode runs successfully, and add a small amount of evidence that clustering can proceed without injecting BLAST-hit references. Documentation changes remain separate in the next commit.
Update the polishing and output documentation to describe cluster_with_reference and clarify how BLAST-derived references participate in clustering. This commit should make it clear that BLAST still runs in both modes, that reference injection into clustering is now optional, and that _withref outputs are intermediate BLAST-filter artifacts rather than unconditional clustering inputs.
…viralmetagenome into optional-ref-clustering
make blast reference injection into clustering optional
Signed-off-by: Joon Klaps <joon.klaps@kuleuven.be>
Cast Lazymaps to Hashmaps to become thread safe
Signed-off-by: Joon Klaps <joon.klaps@kuleuven.be>
Fix undetected conda issues with dev branch
charles-plessy
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I have minor comments, but overall it looks good to me.
| "multiqc": { | ||
| "branch": "master", | ||
| "git_sha": "2c73cc8fa92cf48de3da0b643fdf357a8a290b36", | ||
| "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215", |
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Please document the bump of version in the changelog.
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While we do have the nf-core/modules/multiqc I don't actually use it, we use a local/custom_multiqc where I call the API of multiqc in a python script for custom output formatting. I keep nf-core/modules/multiqc as it's usefull to get all the relevant template updates around it (software versions, custom methods, ...)
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So you don't run multiqc directly in the pipeline?
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No no, I do, It's just wrapped inside a local module.
https://github.com/nf-core/viralmetagenome/blob/dev/modules/local/custom_multiqc/main.nf
The main logic here comes from that we have a 1 sample to many different genome, which highly pollutes the mqc report.html making it sometimes 2-3GB large. So I needed to come up with a solution which was, I keep all important sample specific results within mqc file but combine all genome specific results into overview tables.
reinclude default value of transpose tables
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I advise in removing params from any .nf file except for the root main.nf.
But not blocking for this release
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Yeah... it's someting I've been postponing. I'll make an issue and try and include in the next minor release.
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Signed-off-by: Joon Klaps <joon.klaps@kuleuven.be>
Signed-off-by: Joon Klaps <joon.klaps@kuleuven.be>
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@maxulysse anything else you think i should adresss before this patch release? |
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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).