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Merge pull request #201 from nf-cmgg/dev
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v1.8.1 release PR
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nvnieuwk authored Sep 25, 2024
2 parents add12f7 + 8f64a87 commit aef8a80
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14 changes: 10 additions & 4 deletions CHANGELOG.md
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## v1.8.0 - Optimistic Oostkamp - [September 23 2024]
## v1.8.1 - Open Oostkamp - [September 25 2024]

## New features
### Fixes

1. Revert VEP version to v105

## v1.8.0 - Optimistic Oostkamp - [September 24 2024]

### New features

1. Added `watchpath` functionality to the pipeline. Add the `watch:` prefix to a file basename in the samplesheet and the pipeline will automatically wait for the file to be created in the `--watchdir` directory (the lookup happens recursively)

## Changes
### Changes

1. Bumped the minimal support nextflow version to `24.04.0`
2. Bumped all modules to the newest versions
3. The pipeline now also outputs `csi` indices
4. Rename the `master` branch to `main`
5. Low coverage regions (regions with less than 5 reads) are no longer considered for variant calling

## Refactors
### Refactors

1. Updated the pipeline to the new linting guidelines
2. Removed `check_max` in favor of `resourceLimits`
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6 changes: 4 additions & 2 deletions modules.json
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"ensemblvep/download": {
"branch": "master",
"git_sha": "54c183cba37cac58860d9967feaae54acf9cc3e0",
"installed_by": ["modules"]
"installed_by": ["modules"],
"patch": "modules/nf-core/ensemblvep/download/ensemblvep-download.diff"
},
"ensemblvep/vep": {
"branch": "master",
"git_sha": "54c183cba37cac58860d9967feaae54acf9cc3e0",
"installed_by": ["vcf_annotate_ensemblvep_snpeff"]
"installed_by": ["vcf_annotate_ensemblvep_snpeff"],
"patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff"
},
"gatk4/calibratedragstrmodel": {
"branch": "master",
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34 changes: 34 additions & 0 deletions modules/nf-core/ensemblvep/download/ensemblvep-download.diff

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4 changes: 2 additions & 2 deletions modules/nf-core/ensemblvep/download/main.nf

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35 changes: 35 additions & 0 deletions modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff

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4 changes: 2 additions & 2 deletions modules/nf-core/ensemblvep/vep/main.nf

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2 changes: 1 addition & 1 deletion nextflow.config
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description = """A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data"""
mainScript = 'main.nf'
nextflowVersion = '!>=24.04.0'
version = '1.8.0'
version = '1.8.1'
doi = ''
}

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