From c1c8d3a0c09d61157a0afcb0542701ff1e8d65cd Mon Sep 17 00:00:00 2001
From: Jeremy Mathews <Jeremy.Mathews@utsouthwestern.edu>
Date: Fri, 19 Jul 2019 08:28:20 -0500
Subject: [PATCH] fix biohpc.config typos and add gtf location to astrocyte
params
---
workflow/conf/biohpc.config | 6 +++---
workflow/main.nf | 2 ++
2 files changed, 5 insertions(+), 3 deletions(-)
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index c514d07..7237cad 100644
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -78,21 +78,21 @@ params {
genomesize = 'hs'
chromsizes = '/project/shared/bicf_workflow_ref/GRCh38/genomefile.txt'
fasta = '/project/shared/bicf_workflow_ref/GRCh38/genome.fa'
- gta = '/project/shared/bicf_workflow_ref/GRCh38/gencode.gtf'
+ gtf = '/project/shared/bicf_workflow_ref/GRCh38/gencode.gtf'
}
'GRCh37' {
bwa = '/project/shared/bicf_workflow_ref/GRCh37'
genomesize = 'hs'
chromsizes = '/project/shared/bicf_workflow_ref/GRCh37/genomefile.txt'
fasta = '/project/shared/bicf_workflow_ref/GRCh37/genome.fa'
- gta = '/project/shared/bicf_workflow_ref/GRCh37/gencode.gtf'
+ gtf = '/project/shared/bicf_workflow_ref/GRCh37/gencode.gtf'
}
'GRCm38' {
bwa = '/project/shared/bicf_workflow_ref/GRCm38'
genomesize = 'mm'
chromsizes = '/project/shared/bicf_workflow_ref/GRCm38/genomefile.txt'
fasta = '/project/shared/bicf_workflow_ref/GRCm38/genome.fa'
- gta = '/project/shared/bicf_workflow_ref/GRCm38/gencode.gtf'
+ gtf = '/project/shared/bicf_workflow_ref/GRCm38/gencode.gtf'
}
}
}
diff --git a/workflow/main.nf b/workflow/main.nf
index 8aa4622..193fb27 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -37,6 +37,7 @@ if (params.astrocyte) {
params.bwaIndex = "$referenceLocation/$params.genome"
params.chromSizes = "$referenceLocation/$params.genome/genomefile.txt"
params.fasta = "$referenceLocation/$params.genome/genome.fa"
+ params.gtf = "$referenceLocation/$params.genome/gencode.gtf"
if (params.genome == 'GRCh37' || params.genome == 'GRCh38') {
params.genomeSize = 'hs'
} else if (params.genome == 'GRCm38') {
@@ -47,6 +48,7 @@ if (params.astrocyte) {
params.genomeSize = params.genome ? params.genomes[ params.genome ].genomesize ?: false : false
params.chromSizes = params.genome ? params.genomes[ params.genome ].chromsizes ?: false : false
params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
+ params.gtf = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
}
--
GitLab