From 51ff8a09dccb03433f919fcddc9f29cb3b429b2d Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 13 Jul 2020 20:43:05 -0500
Subject: [PATCH] Fix configs and refs
---
workflow/configs/aws.config | 12 ++++++------
workflow/configs/cluster.config | 14 +++++++-------
workflow/main.nf | 7 +++++--
workflow/nextflow.config | 1 +
4 files changed, 19 insertions(+), 15 deletions(-)
diff --git a/workflow/configs/aws.config b/workflow/configs/aws.config
index 86a5b31..5e28c1e 100644
--- a/workflow/configs/aws.config
+++ b/workflow/configs/aws.config
@@ -12,27 +12,27 @@ process {
cpus = 1
memory = '1 GB'
- withLabel: checkDesignFile {
+ withName: checkDesignFile {
cpus = 2
memory = '1 GB'
}
- withLabel: count211 {
+ withName: count211 {
cpus = 2
memory = '30 GB'
}
- withLabel: count302 {
+ withName: count302 {
cpus = 2
memory = '30 GB'
}
- withLabel: count310 {
+ withName: count310 {
cpus = 2
memory = '30 GB'
}
- withLabel: versions {
+ withName: versions {
cpus = 3
memory = '1 GB'
}
- withLabel: multiqc {
+ withName: multiqc {
cpus = 1
memory = '1 GB'
}
diff --git a/workflow/configs/cluster.config b/workflow/configs/cluster.config
index 4685e9b..457622e 100644
--- a/workflow/configs/cluster.config
+++ b/workflow/configs/cluster.config
@@ -9,25 +9,25 @@ process {
withLabel: checkDesignFile {
executor = 'local'
}
- withLabel: count211 {
+ withName: count211 {
queue = '128GB,256GB,256GBv1,384GB'
}
- withLabel: count220 {
+ withName: count220 {
queue = '128GB,256GB,256GBv1,384GB'
}
- withLabel: count302 {
+ withName: count302 {
queue = '128GB,256GB,256GBv1,384GB'
}
- withLabel: count310 {
+ withName: count310 {
queue = '128GB,256GB,256GBv1,384GB'
}
- withLabel: count400 {
+ withName: count400 {
queue = '128GB,256GB,256GBv1,384GB'
}
- withLabel: versions {
+ withName: versions {
executor = 'local'
}
- withLabel: multiqc {
+ withName: multiqc {
executor = 'local'
}
}
diff --git a/workflow/main.nf b/workflow/main.nf
index 34649e6..b186542 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -22,7 +22,6 @@ params.name = "run"
params.fastq = "test_data/mu.v3s1r500/*.fastq.gz"
params.designFile = "test_data/mu.v3s1r500/design.csv"
params.genome = 'mm10-2020-A'
-params.genomeLocation = '/project/apps_database/cellranger/refdata-gex-'
params.expectCells = 10000
params.forceCells = 0
params.kitVersion = '3GEXv3'
@@ -39,7 +38,11 @@ if (params.kitVersion == "3GEXv3" && params.version == '2.1.1') {
// Define variables if astrocyte (or from config)
if (params.astrocyte) {
print("Running under astrocyte")
- params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-'
+ if (params.version == "4.0.0") {
+ params.genomeLocation = '/project/apps_database/cellranger/refdata-gex-'
+ } else {
+ params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-'
+ }
if (params.kitVersion == "3GEXv1") {
params.chemistryParam ='SC3Pv1'
} else if (params.kitVersion == "3GEXv2") {
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index c402bf3..1ab9a50 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -1,6 +1,7 @@
profiles {
standard {
includeConfig 'configs/biohpc.config'
+ includeConfig 'configs/cluster.config'
}
biohpc {
includeConfig 'configs/biohpc.config'
--
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