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Resolve CW-3327 "Mapping 1 thread"

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This commit is contained in:
Neil Horner 2024-01-18 19:40:14 +00:00
parent fbd1bf819c
commit f111755d12
2 changed files with 5 additions and 1 deletions
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4
CHANGELOG.md
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@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## [Unreleased]
### Fixed
- Mapping stage using a single thread only.
## [v1.0.0] ## [v1.0.0]
### Added ### Added
- Published minimap2 and pychopper results to output directory. - Published minimap2 and pychopper results to output directory.

2
subworkflows/reference_assembly.nf
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@ -22,7 +22,7 @@ process map_reads{
RightShift: ${params.poly_context}, RegexEnd: "[Aa]{${params.max_poly_run},}", RightShift: ${params.poly_context}, RegexEnd: "[Aa]{${params.max_poly_run},}",
Stranded: True,Invert: True, Tsv: "internal_priming_fail.tsv"} """ Stranded: True,Invert: True, Tsv: "internal_priming_fail.tsv"} """
def mm2_threads = Math.min(task.cpus - 3, 1) def mm2_threads = Math.max(task.cpus - 3, 1)
""" """
minimap2 -t ${mm2_threads} -ax splice ${params.minimap2_opts} ${index} ${fastq_reads}\ minimap2 -t ${mm2_threads} -ax splice ${params.minimap2_opts} ${index} ${fastq_reads}\
| samtools view -q ${params.minimum_mapping_quality} -F 2304 -Sb -\ | samtools view -q ${params.minimum_mapping_quality} -F 2304 -Sb -\