First pipeline release - #54
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Inactivate DiMSum error modelling step (mainly for small test data set)
Heatmap: reversing aa order
Latest README and example file updates for nf-core review
A few more README.md changes
…r-correction Major Update
…r-correction edited singularity conatiners
…r-correction report, snapshot, seqdepth calculation efficiency
…r-correction conda package versions updated & test snapshot
…r-correction updated report
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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: 4.0.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
improved false-double variant filtering
min_counts (1) and base_qual (40) were changed in nextflow.config but not in the schema, which fails the nf-core lint check nextflow_config/config_defaults. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Two small robustness fixes, both leaving the estimator's logic unchanged: * lm() is fitted on the finite rows only. .usable is already computed directly above and the guard already tests it, but the fit ran on the full vector, so a single -Inf (log of a zero-coverage double) aborted it with 'NA/NaN/Inf in y'. R's default na.action=na.omit already drops NA rows, so pre-subsetting gives identical coefficients wherever the fit currently succeeds; it only differs where lm() errors out today. The distance range is captured beforehand so the coverage lookup cannot end up shorter than the distances it is queried with. * counts_per_cov_corrected is clamped at zero. The existing guard zeroes both columns but tests the *rounded* count, so a subtraction landing in (-0.5, 0] rounds to 0, skips the guard, and leaves a negative frequency behind. This completes the intent already stated in the code comment. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
The nf-test job fails while pulling the multiqc image with 'failed to register layer: no space left on device' (docker exit 125). The pipeline pulls ~17 container images, three of them heavy bioconductor/R stacks (mutscan, DiMSum), which overruns the runner disk part-way through. Reclaim the preinstalled toolchain before anything is downloaded. The RunsOn default image is ubuntu24-full-x64, so the same Android/.NET/Haskell bloat as a GitHub-hosted runner is present and removable. The action SHA is the one already pinned in download_pipeline.yml. If this proves insufficient, the next lever is a larger runner volume via a 'volume=80gb' label on the nf-test job.
Fix/pr62 lint and snapshot
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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).