From a1c370ff6d14b89aacadb086ed1dde7ef62b27ae Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Tue, 12 Feb 2019 21:11:22 -0600
Subject: [PATCH] update skip dea

---
 astrocyte_pkg.yml | 6 +++---
 workflow/main.nf  | 5 +++--
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index f74af09..ded1127 100644
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -158,9 +158,9 @@ workflow_parameters:
   - id: genome
     type: select
     choices:
-      - [ '/project/shared/bicf_workflow_ref/GRCh38', 'Human GRCh38']
-      - [ '/project/shared/bicf_workflow_ref/GRCh37', 'Human GRCh37']
-      - [ '/project/shared/bicf_workflow_ref/GRCm38', 'Mouse GRCm38']
+      - [ '/project/shared/bicf_workflow_ref/human/GRCh38', 'Human GRCh38']
+      - [ '/project/shared/bicf_workflow_ref/human/GRCh37', 'Human GRCh37']
+      - [ '/project/shared/bicf_workflow_ref/mouse/GRCm38', 'Mouse GRCm38']
     required: true
     description: |
       Reference genome for alignment
diff --git a/workflow/main.nf b/workflow/main.nf
index 6fe1ddd..5158e81 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -6,7 +6,7 @@ params.output= "$baseDir/output"
 params.fastqs="$params.input/*.fastq.gz"
 params.design="$params.input/design.txt"
 
-params.genome="/project/shared/bicf_workflow_ref/GRCh38/"
+params.genome="/project/shared/bicf_workflow_ref/human/GRCh38/"
 params.markdups="picard"
 params.stranded="0"
 params.pairs="pe"
@@ -20,7 +20,8 @@ fastqs=file(params.fastqs)
 design_file = file(params.design)
 gtf_file = file("$params.genome/gencode.gtf")
 genenames = file("$params.genome/genenames.txt")
-geneset = file("$params.genome/gsea_gmt/$params.geneset")
+
+geneset = file("$params.genome/../gsea_gmt/$params.geneset")
 dbsnp="$params.genome/dbSnp.vcf.gz"
 indel="$params.genome/GoldIndels.vcf.gz"
 knownindel=file(indel)
-- 
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