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🟡 Changes recommended
The module currently disables -e/pipefail in a way that can mask real task failures, and the updated invocation changes sampling/filters in ways that need confirmation to match intended pipeline behavior.
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Pull request overview
This PR updates the tasmanian Nextflow module to use tasmanian-mismatch version 2.0.5, adapting the process to a new/updated CLI while keeping the same output artifact (${library}.tasmanian.csv) for downstream aggregation in the EM-seq pipeline.
Changes:
- Bump
bioconda::tasmanian-mismatchto2.0.5and remove the explicitsamtoolsdependency from the process conda env. - Switch from a
samtools view | head | run_tasmanianpipeline to a directtasmanian-mismatchinvocation with explicit filtering flags. - Update versions reporting for MultiQC to reference
tasmanian-mismatch(currently via a static placeholder string).
File summaries
| File | Description |
|---|---|
| modules/tasmanian.nf | Updates the tasmanian stats process to run tasmanian-mismatch 2.0.5 directly and adjusts version reporting/output generation accordingly. |
Review details
- Files reviewed: 1/1 changed files
- Comments generated: 3
- Review effort level: Lite
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| tasmanian-mismatch ${bam} ${genome_fa} \ | ||
| --position-mode read \ | ||
| --min-base-quality 20 \ | ||
| --min-map-quality 30 \ | ||
| -F 3840 \ |
| tuple val(library), path("${library}.tasmanian.csv"), emit: for_agg | ||
| tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -n 1 | sed \'s/^samtools //\''), topic: versions | ||
| tuple val("${task.process}"), val('tasmanian'), val('*should be* 1.0.9'), topic: versions | ||
| tuple val("${task.process}"), val('tasmanian-mismatch'), val('*should be* 2.0.5'), topic: versions |
| set +e | ||
| set +o pipefail |
|
let's deploy that branch so we can gain experience. |
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