updating process scripts

19ca68db · Brandi Cantarel · e550dccd · 19ca68db · 19ca68db · 75a4aa68
Commit 19ca68db authored Nov 09, 2018 by Brandi Cantarel
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README.md README.md +1 -1

workflow/main.nf workflow/main.nf +2 -1

workflow/process_scripts workflow/process_scripts +1 -1

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--- a/README.md
+++ b/README.md
 ## RNASeq Analysis Worklow

 ```
-module load nextflow/0.24.1-SNAPSHOT
+module load nextflow
 nextflow run workflow/main.nf
 ```
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -201,14 +201,15 @@ process statanal {
  file "*.txt" into txtfiles
  file "*.png" into psfiles
  file("bg.rda") into rdafiles
+  file("geneset.shiny.gmt") into gmtfile
  when:
  script:
  if (params.dea == 'skip')
-  """
  perl $baseDir/scripts/concat_cts.pl -o ./ *.cts
  perl $baseDir/scripts/concat_fpkm.pl -o ./ *.fpkm.txt
  touch empty.png
  touch bg.rda
+  cp geneset.gmt geneset.shiny.gmt
  """
  else
  """

--- a/process_scripts @ 75a4aa68
+++ b/process_scripts @ 75a4aa68
-Subproject commit 636e989b65cc76352111cedac9a8762fbe570384
+Subproject commit 75a4aa688f82c607794e109e4ee0ec8e12418a2d