From 3d24ed7efaf50c8185e3f19200a00d79c690002b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 4 Mar 2019 23:46:20 -0600
Subject: [PATCH] Make reference folder follow standard to fix #2
---
astrocyte_pkg.yml | 18 +++++++++---------
workflow/conf/biohpc.config | 33 +++++++++++++++++++++++++++++++++
workflow/main.nf | 6 ++++--
3 files changed, 46 insertions(+), 11 deletions(-)
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index ccabafa..e4ab49f 100755
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -97,15 +97,15 @@ workflow_parameters:
- id: genome
type: select
choices:
- - [ 'refdata-cellranger-GRCh38-3.0.0', 'Human GRCh38 release 93']
- - [ 'refdata-cellranger-GRCh38-1.2.0', 'Human GRCh38 release 84']
- - [ 'refdata-cellranger-hg19-3.0.0', 'Human GRCh37 (hg19) release 87']
- - [ 'refdata-cellranger-hg19-1.2.0', 'Human GRCh37 (hg19) release 84']
- - [ 'refdata-cellranger-mm10-3.0.0', 'Mouse GRCm38 (mm10) release 93']
- - [ 'refdata-cellranger-mm10-1.2.0', 'Mouse GRCm38 (mm10) release 84']
- - [ 'refdata-cellranger-hg19_and_mm10-3.0.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 93']
- - [ 'refdata-cellranger-hg19_and_mm10-1.2.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 84']
- - [ 'refdata-cellranger-ercc92-1.2.0', 'ERCC.92 Spike-In']
+ - [ 'GRCh38-3.0.0', 'Human GRCh38 release 93']
+ - [ 'GRCh38-1.2.0', 'Human GRCh38 release 84']
+ - [ 'hg19-3.0.0', 'Human GRCh37 (hg19) release 87']
+ - [ 'hg19-1.2.0', 'Human GRCh37 (hg19) release 84']
+ - [ 'mm10-3.0.0', 'Mouse GRCm38 (mm10) release 93']
+ - [ 'mm10-1.2.0', 'Mouse GRCm38 (mm10) release 84']
+ - [ 'hg19_and_mm10-3.0.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 93']
+ - [ 'hg19_and_mm10-1.2.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 84']
+ - [ '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 66ffcf2..4b18a46 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -18,6 +18,39 @@ process {
}
}
+params {
+ // Reference file paths on BioHPC
+ genomes {
+ 'GRCh38-3.0.0' {
+ loc = '/project/apps_database/cellranger/refdata-cellranger-'
+ }
+ 'GRCh38-1.2.0' {
+ loc = '/project/apps_database/cellranger/refdata-cellranger-'
+ }
+ 'hg19-3.0.0' {
+ loc = '/project/apps_database/cellranger/refdata-cellranger-'
+ }
+ 'hg19-1.2.0' {
+ loc = '/project/apps_database/cellranger/refdata-cellranger-'
+ }
+ 'mm10-3.0.0' {
+ loc = '/project/apps_database/cellranger/refdata-cellranger-'
+ }
+ 'mm10-1.2.0' {
+ loc = '/project/apps_database/cellranger/refdata-cellranger-'
+ }
+ 'hg19_and_mm10-3.0.0' {
+ loc = '/project/apps_database/cellranger/refdata-cellranger-'
+ }
+ 'hg19_and_mm10-1.2.0' {
+ loc = '/project/apps_database/cellranger/refdata-cellranger-'
+ }
+ 'ercc92-1.2.0' {
+ loc = '/project/apps_database/cellranger/refdata-cellranger-'
+ }
+ }
+}
+
trace {
enabled = true
file = 'pipeline_trace.txt'
diff --git a/workflow/main.nf b/workflow/main.nf
index 7d634a2..4072b26 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -6,7 +6,9 @@
// Define Input variables
params.fastq = "$baseDir/../test_data/*.fastq.gz"
params.designFile = "$baseDir/../test_data/design.csv"
-params.genome = 'refdata-cellranger-GRCh38-1.2.0'
+params.genome = 'GRCh38-1.2.0'
+params.genomes = []
+params.genomeLocation = params.genome ? params.genomes[ params.genome ].loc ?: false : false
params.expectCells = 10000
params.forceCells = 0
params.version = '3.0.2'
@@ -21,7 +23,7 @@ fastqList = Channel
.map { file -> [ file.getFileName().toString(), file.toString() ].join("\t") }
.collectFile(name: 'fileList.tsv', newLine: true)
refLocation = Channel
- .fromPath('/project/apps_database/cellranger/'+params.genome)
+ .fromPath(params.genomeLocation+params.genome)
.ifEmpty { exit 1, "referene not found: ${params.genome}" }
expectCells = params.expectCells
forceCells = params.forceCells
--
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