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process_beds: optimize for HyperCap data #288

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Merged
merged 2 commits into from
Oct 1, 2025
Merged

process_beds: optimize for HyperCap data #288

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9ba6579
process_beds: optimize for HyperCap data
ToonRosseel Oct 1, 2025
0a8f25d
fix
ToonRosseel Oct 1, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## Changes

1. Renamed the `tbi` samplesheet field to `gtbi` to make it more clear that this is the index of the GVCF file.
2. Process_bed module: add sorting step + git HyperCap profile more memory.

## v1.11.0 - Generous Ghent - [Sept 1 2025]

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5 changes: 5 additions & 0 deletions conf/hypercap.config
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Expand Up @@ -9,3 +9,8 @@ params {
scatter_count = 5
only_pass = true
}
process {
withName: PROCESS_BEDS {
memory = 64.GB
}
}
1 change: 1 addition & 0 deletions modules/local/process_beds/main.nf
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Expand Up @@ -27,6 +27,7 @@ process PROCESS_BEDS {
"""
${unzip} ${bed} \\
| grep ${args} \\
| bedtools sort -faidx ${fai} \\
| bedtools merge ${args2} \\
${intersect} \\
> ${prefix}.bed
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