Bump tasmanian 2.0.4 production emseq v2 - #73
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🟡 Changes recommended
There are correctness/consistency issues in the updated fastp invocation/version reporting, the workflow_name_modifier usage, and the Tasmanian version/performance changes need alignment with the PR intent.
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Pull request overview
Updates pipeline tooling and reporting to align with newer Tasmanian-Mismatch usage and to enrich NEB aggregation metadata, plus adds configurability for invoking fastp from a custom location.
Changes:
- Update
tasmanianmodule to usetasmanian-mismatchv2 CLI and pin the conda package accordingly. - Add optional
params.fastp_pathsupport for runningfastpfrom a specified location. - Extend
aggregate_resultsto accept workflow version and workflow name modifier as explicit inputs/CLI flags.
File summaries
| File | Description |
|---|---|
| modules/tasmanian.nf | Pins tasmanian-mismatch and switches to the v2 invocation style / args. |
| modules/fastp.nf | Adds configurable prefix/path for invoking fastp. |
| modules/aggregate_results.nf | Adds workflow metadata inputs and forwards them to aggregate_results.rb. |
| main.nf | Updates the aggregate_results call signature and provides new metadata values. |
| conf/test.config | Adds fastp_path to the test profile params. |
Review details
- Files reviewed: 5/5 changed files
- Comments generated: 5
- Review effort level: Lite
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| tuple val("${task.process}"), val('fastp'), eval('fastp --version 2>&1 | cut -f 2 -d " "'), topic: versions | ||
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| script: | ||
| def fastp_path = params.fastp_path ? params.fastp_path : '' |
| tuple val(library), path("${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* 2.0.3'), topic: versions |
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| tasmanian-mismatch ${bam} ${genome_fa} \ | ||
| --position-mode read \ | ||
| --min-base-quality 20 \ | ||
| --min-map-quality 30 \ | ||
| -F 3840 \ |
| workflow_name_modifier = params.workflow_name_modifier ? "-${params.workflow_name_modifier}" : "" | ||
| aggregate_results( agg_tuple, "${params.workflow}${workflow_name_modifier}" ) | ||
| } | ||
| aggregate_results( agg_tuple, "${params.workflow}", 'unspecified', params.workflow_name_modifier ?: '' ) |
| tag { library } | ||
| publishDir "${params.outputDir}/stats/tasmanian" | ||
| conda "bioconda::samtools=1.22 bioconda::tasmanian-mismatch=1.0.9" | ||
| conda "bioconda::tasmanian-mismatch=2.0.3" |
Contributor
Author
|
THis was a mistake. THere is a previous PR that's doing this |
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