Merge pull request #354 from jfnavarro/tumoronly

Tumor-only mode for Mutect2 and MSIsensor
nf-core · Mar 10, 2021 · 7c44773 · 7c44773
2 parents f473afe + d68befa
commit 7c44773
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Showing 3 changed files with 162 additions and 72 deletions.
diff --git a/conf/base.config b/conf/base.config
@@ -97,4 +97,7 @@ process {
     container = {(params.annotation_cache && params.vep_cache) ? 'nfcore/sarek:dev' : "nfcore/sarekvep:dev.${params.genome}"}
     errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
   }
+  withLabel:msisensor {
+    container = "quay.io/biocontainers/msisensor-pro:1.1.a--hb3646a4_0"
+  }
 }
diff --git a/environment.yml b/environment.yml
@@ -38,4 +38,4 @@ dependencies:
   - bioconda::vcfanno=0.3.2=0
   - bioconda::vcftools=0.1.16=he513fc3_4
   - conda-forge::pigz=2.3.4=hed695b0_1
-  - conda-forge::r-ggplot2=3.3.0=r40h6115d3f_1
+  - conda-forge::r-ggplot2=3.3.0=r40h6115d3f_1