From 2ada067dd520900d86c11dd1316008b3f48f366d Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 7 Sep 2018 14:47:47 -0500
Subject: [PATCH] Hardwire ref genome locations into astrocyte yml
---
astrocyte_pkg.yml | 10 +++++-----
workflow/conf/biohpc.config | 21 ---------------------
workflow/main.nf | 20 ++++----------------
3 files changed, 9 insertions(+), 42 deletions(-)
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index e896602..095101c 100755
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -95,11 +95,11 @@ workflow_parameters:
- id: genome
type: select
choices:
- - [ 'GRCh38', 'Human GRCh38']
- - [ 'hg19', 'Human GRCh37 (hg19)']
- - [ 'mm10', 'Mouse GRCm38 (mm10)']
- - [ 'hg19.mm10', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19)']
- - [ 'ercc92', 'ERCC.92 Spike-In']
+ - [ '/project/apps_database/cellranger/refdata-cellranger-GRCh38-1.2.0', 'Human GRCh38']
+ - [ '/project/apps_database/cellranger/refdata-cellranger-hg19-1.2.0', 'Human GRCh37 (hg19)']
+ - [ '/project/apps_database/cellranger/refdata-cellranger-mm10-1.2.0', 'Mouse GRCm38 (mm10)']
+ - [ '/project/apps_database/cellranger/refdata-cellranger-hg19_and_mm10-1.2.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19)']
+ - [ '/project/apps_database/cellranger/refdata-cellranger-ercc92-1.2.0', 'ERCC.92 Spike-In']
required: true
description: |
Reference species and genome used for alignment and subsequent analysis.
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index f6cb1ed..fbaca91 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -12,27 +12,6 @@ process {
}
}
-params {
- // Reference file paths on BioHPC
- genomes {
- 'ercc92' {
- ref = '/project/apps_database/cellranger/refdata-cellranger-ercc92-1.2.0'
- }
- 'GRCh38' {
- ref = '/project/apps_database/cellranger/refdata-cellranger-GRCh38-1.2.0'
- }
- 'hg19' {
- ref = '/project/apps_database/cellranger/refdata-cellranger-hg19-1.2.0'
- }
- 'mm10' {
- ref = '/project/apps_database/cellranger/refdata-cellranger-mm10-1.2.0'
- }
- 'hg19.mm10' {
- ref = '/project/apps_database/cellranger/refdata-cellranger-hg19_and_mm10-1.2.0'
- }
- }
-}
-
trace {
enabled = true
file = 'pipeline_trace.txt'
diff --git a/workflow/main.nf b/workflow/main.nf
index fac7a70..f4f5369 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -6,25 +6,10 @@
// Define Input variables
params.fastq = "$baseDir/../test_data/*.fastq.gz"
params.designFile = "$baseDir/../test_data/design.csv"
-params.genome = 'GRCh38'
-params.genomes = []
-params.ref = params.genome ? params.genomes[ params.genome ].ref ?: false : false
+params.genome = '/project/apps_database/cellranger/refdata-cellranger-GRCh38-1.2.0'
params.expectCells = 10000
params.forceCells = 0
-println params.genome
-println params.genomes[ params.genome ].ref
-println params.ref
-
-// Check inputs
-if( params.ref ){
- refLocation = Channel
- .fromPath(params.ref)
- .ifEmpty { exit 1, "referene not found: ${params.ref}" }
-} else {
- exit 1, "No reference genome specified."
-}
-
// Define List of Files
fastqList = Channel
.fromPath(params.fastq)
@@ -33,6 +18,9 @@ fastqList = Channel
.collectFile(name: 'fileList.tsv', newLine: true)
// Define regular variables
+refLocation = Channel
+ .fromPath(params.genome)
+ .ifEmpty { exit 1, "referene not found: ${params.genome}" }
expectCells = params.expectCells
forceCells = params.forceCells
--
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