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Make the QUARTONOTEBOOK module handle collected data (samples) instead of working in a per-sample basis, as multiple inputs are desired for the QC reporting. The changes are applied through a module patch.
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I think this is ready for review now. I'll need some help with updating snapshots, as neither my local system nor the HPC I have access to yields the same snapshots as GHA due to the previously discussed rounding issues. Currently, this PR doesn't touch the existing MultiQC report, but this could be added if desired. One alternative would be to remove all the figures/tables currently included in the MultiQC report, but still keep it for keeping track of module versions, workflow summary, etc. - I don't think it should be removed entirely. |
fixed: profile test_full had obsolete implementation of celldex refer…
Pixified: Much smaller container footprint
Disable OpenMP CPU topology detection for MacOS compatibility
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This PR adds an HTML QC report using Quarto. It currently takes the available outputs of the pipeline and collects them into a single, curated report, along with small explanations and the nf-core visual identity. More functionality is desired, but will require changes/additions to the pipeline itself (e.g. adding ribosomal content), so will be added in future PRs.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).