Conversation
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
Member
|
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
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
4 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Do not merge! This is a PR of
devcompared to theTEMPLATEbranch for whole-pipeline reviewing purposes.Changes should be made to
devand this PR should not be merged!