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Fix snpEff report (issue with link to txt file) #110

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Feb 4, 2020
Merged

Fix snpEff report (issue with link to txt file) #110

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fc114bd
fix #106
maxulysse Feb 3, 2020
d6a6878
Merge branch 'dev' into SnpEff
apeltzer Feb 3, 2020
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -25,6 +25,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a

- [#83](https://github.com/nf-core/sarek/pull/83) - Fix some typos in `docs/input.md`
- [#107](https://github.com/nf-core/sarek/pull/107) - Fix linting
- [#110](https://github.com/nf-core/sarek/pull/110) - Fix `snpEff` report issue cf [#106](https://github.com/nf-core/sarek/issues/106)

### `Deprecated`

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2 changes: 1 addition & 1 deletion docs/output.md
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Expand Up @@ -598,7 +598,7 @@ For all samples:
- RAW statistics used by MultiQC
- `VariantCaller_Sample_snpEff.html`
- Statistics to be visualised with a web browser
- `VariantCaller_Sample_snpEff.txt`
- `VariantCaller_Sample_snpEff.genes.txt`
- TXT (tab separated) summary counts for variants affecting each transcript and gene

For further reading and documentation see the [snpEff manual](http://snpeff.sourceforge.net/SnpEff_manual.html#outputSummary)
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3 changes: 1 addition & 2 deletions main.nf
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Expand Up @@ -2949,7 +2949,7 @@ process Snpeff {
val snpeffDb from ch_snpeff_db

output:
set file("${reducedVCF}_snpEff.txt"), file("${reducedVCF}_snpEff.html"), file("${reducedVCF}_snpEff.csv") into snpeffReport
set file("${reducedVCF}_snpEff.genes.txt"), file("${reducedVCF}_snpEff.html"), file("${reducedVCF}_snpEff.csv") into snpeffReport
set variantCaller, idSample, file("${reducedVCF}_snpEff.ann.vcf") into snpeffVCF

when: 'snpeff' in tools || 'merge' in tools
Expand All @@ -2969,7 +2969,6 @@ process Snpeff {
> ${reducedVCF}_snpEff.ann.vcf

mv snpEff_summary.html ${reducedVCF}_snpEff.html
mv ${reducedVCF}_snpEff.genes.txt ${reducedVCF}_snpEff.txt
"""
}

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