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nf-core · Mar 20, 2020 · e6c693f · e6c693f
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diff --git a/docs/output.md b/docs/output.md
@@ -445,7 +445,7 @@ cases.
 For further reading see the [MSIsensor paper](https://www.ncbi.nlm.nih.gov/pubmed/24371154).
 
 For a Tumor/Normal pair only:
-**Output directory: `results/[TUMORSAMPLE]_vs_[NORMALSAMPLE]/MSIsensor`**
+**Output directory: `results/VariantCalling/[TUMORSAMPLE]_vs_[NORMALSAMPLE]/MSIsensor`**
 
 - `[TUMORSAMPLE]_vs_[NORMALSAMPLE]`_msisensor
   - MSI score output, contains information about the number of somatic sites.

diff --git a/main.nf b/main.nf
@@ -2642,7 +2642,7 @@ process msisensor {
 
     tag {idSampleTumor + "_vs_" + idSampleNormal}
 
-    publishDir "${params.outdir}/${idSampleTumor}_vs_${idSampleNormal}/MSIsensor", mode: params.publishDirMode
+    publishDir "${params.outdir}/VariantCalling/${idSampleTumor}_vs_${idSampleNormal}/MSIsensor", mode: params.publishDirMode
 
     input:
     set idPatient, idSampleNormal, file(bamNormal), file(baiNormal), idSampleTumor, file(bamTumor), file(baiTumor) from pairBamMsisensor