8000 Add SnpEff to full sized tests by FriederikeHanssen · Pull Request #1330 · nf-core/sarek · GitHub
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Add SnpEff to full sized tests #1330

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Merged
merged 2 commits into from
Nov 15, 2023
Merged

Add SnpEff to full sized tests #1330

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0d36a50
Add SnpEff to full sized tests
FriederikeHanssen Nov 15, 2023
c46c354
Merge branch 'dev' into fix_fulltest
FriederikeHanssen Nov 15, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -43,6 +43,7 @@ Pårtetjåkko is a mountain in the south of the park.
- [#1325](https://github.com/nf-core/sarek/pull/1325) - Update bcfannotate tests and related config files
- [#1328](https://github.com/nf-core/sarek/pull/1328) - Fix links to docs in `nextflow_schema.json` and `docs/output.md`
- [#1328](https://github.com/nf-core/sarek/pull/1328) - Add missing icons in `nextflow_schema.json`
- [#1330](https://github.com/nf-core/sarek/pull/1330) - Add SnpEff to full sized tests

### Removed

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2 changes: 1 addition & 1 deletion conf/test_full.config
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Expand Up @@ -18,7 +18,7 @@ params {
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/HCC1395_WXS_somatic_full_test.csv'

// Other params
tools = 'strelka,mutect2,freebayes,ascat,manta,cnvkit,tiddit,controlfreec,vep,ngscheckmate'
tools = 'ngscheckmate,strelka,mutect2,freebayes,ascat,manta,cnvkit,tiddit,controlfreec,vep,snpeff'
split_fastq = 20000000
intervals = 's3://ngi-igenomes/test-data/sarek/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed'
wes = true
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2 changes: 1 addition & 1 deletion conf/test_full_germline.config
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Expand Up @@ -18,6 +18,6 @@ params {
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/NA12878_WGS_30x_full_test.csv'

// Other params
tools = 'strelka,freebayes,haplotypecaller,deepvariant,manta,tiddit,cnvkit,vep'
tools = 'strelka,freebayes,haplotypecaller,deepvariant,manta,tiddit,cnvkit,vep,snpeff'
split_fastq = 50000000
}
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