Commit 19ca68db authored by Brandi Cantarel's avatar Brandi Cantarel

updating process scripts

parent e550dccd
Pipeline #2594 failed with stage
## RNASeq Analysis Worklow ## RNASeq Analysis Worklow
``` ```
module load nextflow/0.24.1-SNAPSHOT module load nextflow
nextflow run workflow/main.nf nextflow run workflow/main.nf
``` ```
...@@ -201,14 +201,15 @@ process statanal { ...@@ -201,14 +201,15 @@ process statanal {
file "*.txt" into txtfiles file "*.txt" into txtfiles
file "*.png" into psfiles file "*.png" into psfiles
file("bg.rda") into rdafiles file("bg.rda") into rdafiles
file("geneset.shiny.gmt") into gmtfile
when: when:
script: script:
if (params.dea == 'skip') if (params.dea == 'skip')
"""
perl $baseDir/scripts/concat_cts.pl -o ./ *.cts perl $baseDir/scripts/concat_cts.pl -o ./ *.cts
perl $baseDir/scripts/concat_fpkm.pl -o ./ *.fpkm.txt perl $baseDir/scripts/concat_fpkm.pl -o ./ *.fpkm.txt
touch empty.png touch empty.png
touch bg.rda touch bg.rda
cp geneset.gmt geneset.shiny.gmt
""" """
else else
""" """
......
Subproject commit 636e989b65cc76352111cedac9a8762fbe570384 Subproject commit 75a4aa688f82c607794e109e4ee0ec8e12418a2d
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