Merge pull request #682 from mskcc/correctMafSize

correct mafSize

pipeline.nf

@@ -1855,6 +1855,7 @@ process SomaticFacetsAnnotation {
   output:
     set idTumor, idNormal, target, file("${outputPrefix}.facets.zygosity.maf"), file("${outputPrefix}.armlevel.unfiltered.txt") into FacetsAnnotationOutputs
     set file("${outputPrefix}.armlevel.unfiltered.txt"), file("${outputPrefix}.genelevel.unfiltered.txt") into FacetsArmGeneOutputs
+    file("file-size.txt") into mafSize
 
   when: tools.containsAll(["facets", "mutect2", "manta", "strelka2"]) && runSomatic
 
@@ -1884,6 +1885,7 @@ process SomaticFacetsAnnotation {
   sed -i -e s@${idTumor}@${outputPrefix}@g ${outputPrefix}.armlevel.unfiltered.txt
 
   Rscript --no-init-file /usr/bin/annotate-with-zygosity-somatic.R ${outputPrefix}.facets.maf ${outputPrefix}.facets.zygosity.maf
+  echo -e "${outputPrefix}\t`wc -l ${outputPrefix}.facets.zygosity.maf | cut -d ' ' -f1`" > file-size.txt
   """
 }
 
@@ -1917,7 +1919,6 @@ process RunNeoantigen {
 
   output:
     set idTumor, idNormal, target, file("${outputDir}/*") into neoantigenOut
-    file("file-size.txt") into mafSize
     file("${idTumor}__${idNormal}.all_neoantigen_predictions.txt") into NetMhcStatsOutput
     file("${outputDir}/*.maf") into NeoantigenMafOutput
 
@@ -1942,7 +1943,6 @@ process RunNeoantigen {
   tmpDir = "${outputDir}-tmp"
   tmpDirFullPath = "\$PWD/${tmpDir}/"  // must set full path to tmp directories for netMHC and netMHCpan to work; for some reason doesn't work with /scratch, so putting them in the process workspace
   """
-  echo -e "${outputPrefix}\t`wc -l ${mafFile} | cut -d ' ' -f1`" > file-size.txt
   export TMPDIR=${tmpDirFullPath}
   mkdir -p ${tmpDir}
   chmod 777 ${tmpDir}