fix nf-core#106

maxulysse · Feb 3, 2020 · fc114bd · fc114bd
1 parent e7852b3
commit fc114bd
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -24,6 +24,7 @@ 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`
 

diff --git a/docs/output.md b/docs/output.md
@@ -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)

diff --git a/main.nf b/main.nf
@@ -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
@@ -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
     """
 }