From fd8f3ac60678962bb25fd1a30e4602bbdf95809c Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 4 Mar 2019 15:23:53 -0600
Subject: [PATCH] Add 3.0.2 as a param option in astrocyte-pkg.yml, main.nf and
biohpc.config to address #8
---
astrocyte_pkg.yml | 8 +--
workflow/conf/biohpc.config | 7 ++-
workflow/main.nf | 98 +++++++++++++++++++++++++------------
3 files changed, 77 insertions(+), 36 deletions(-)
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index 8181364..492039e 100755
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -42,6 +42,7 @@ workflow_modules:
- 'python/3.6.1-2-anaconda'
- 'cellranger/2.1.1'
- 'cellranger/3.0.1'
+ - 'cellranger/3.0.2'
- 'bcl2fastq/2.17.1.14'
# A list of parameters used by the workflow, defining how to present them,
@@ -125,10 +126,11 @@ workflow_parameters:
- id: version
type: select
- default: 3.0.1
+ default: 3.0.2
choices:
- - [ 3, '3.0.1']
- - [ 2, '2.0.1']
+ - [ 3.0.2, '3.0.2']
+ - [ 3.0.1, '3.0.1']
+ - [ 2.1.1, '2.1.1']
required: true
description: |
10x cellranger version.
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 0b515ec..66ffcf2 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -7,12 +7,15 @@ process {
module = ['python/3.6.1-2-anaconda']
executor = 'local'
}
- $count2 {
+ $count211 {
module = ['cellranger/2.1.1']
}
- $count3 {
+ $count301 {
module = ['cellranger/3.0.1']
}
+ $count302 {
+ module = ['cellranger/3.0.2']
+ }
}
trace {
diff --git a/workflow/main.nf b/workflow/main.nf
index 0165884..2e15c89 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -9,7 +9,7 @@ params.designFile = "$baseDir/../test_data/design.csv"
params.genome = '/project/apps_database/cellranger/refdata-cellranger-GRCh38-1.2.0'
params.expectCells = 10000
params.forceCells = 0
-params.version = 3
+params.version = 3.0.2
// Define regular variables
designLocation = Channel
@@ -56,76 +56,112 @@ samples = designPaths
// Duplicate variables
samples.into {
- samples2
- samples3
+ samples211
+ samples301
+ samples302
}
refLocation.into {
- refLocation2
- refLocation3
+ refLocation211
+ refLocation301
+ refLocation302
}
-expectCells2 = expectCells
-expectCells3 = expectCells
-forceCells2 = forceCells
-forceCells3 = forceCells
-process count2 {
- tag "count2-$sample"
+expectCells211 = expectCells
+expectCells301 = expectCells
+expectCells302 = expectCells
+forceCells211 = forceCells
+forceCells301 = forceCells
+forceCells302 = forceCells
+
+process count211 {
+ tag "count211-$sample"
+
+ publishDir "$baseDir/output", mode: 'copy'
+
+ input:
+
+ set sample, file("${sample}_S1_L00?_R1_001.fastq.gz"), file("${sample}_S1_L00?_R2_001.fastq.gz") from samples211
+ file ref from refLocation211.first()
+ expectCells211
+ forceCells211
+
+ output:
+
+ file("**/outs/**") into outPaths211
+
+ when:
+ version == 211
+
+ script:
+ if (forceCells211 == 0){
+ """
+ cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells211
+ """
+ } else {
+ """
+ cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells211
+ """
+ }
+}
+
+process count301 {
+ tag "count301-$sample"
publishDir "$baseDir/output", mode: 'copy'
input:
- set sample, file("${sample}_S1_L00?_R1_001.fastq.gz"), file("${sample}_S1_L00?_R2_001.fastq.gz") from samples2
- file ref from refLocation2.first()
- expectCells2
- forceCells2
+ set sample, file("${sample}_S1_L00?_R1_001.fastq.gz"), file("${sample}_S1_L00?_R2_001.fastq.gz") from samples301
+ file ref from refLocation301.first()
+ expectCells301
+ forceCells301
output:
- file("**/outs/**") into outPaths2
+ file("**/outs/**") into outPaths301
when:
- version == 2
+ version == 301
script:
- if (forceCells2 == 0){
+ if (forceCells301 == 0){
"""
- cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells2
+ cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells301
"""
} else {
"""
- cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells2
+ cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells301
"""
}
}
-process count3 {
- tag "count3-$sample"
+process count302 {
+ tag "count302-$sample"
publishDir "$baseDir/output", mode: 'copy'
input:
- set sample, file("${sample}_S1_L00?_R1_001.fastq.gz"), file("${sample}_S1_L00?_R2_001.fastq.gz") from samples3
- file ref from refLocation3.first()
- expectCells3
- forceCells3
+ set sample, file("${sample}_S1_L00?_R1_001.fastq.gz"), file("${sample}_S1_L00?_R2_001.fastq.gz") from samples302
+ file ref from refLocation302.first()
+ expectCells302
+ forceCells302
output:
- file("**/outs/**") into outPaths3
+ file("**/outs/**") into outPaths302
when:
- version == 3
+ version == 302
script:
- if (forceCells3 == 0){
+ if (forceCells302 == 0){
"""
- cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells3
+ cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells302
"""
} else {
"""
- cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells3
+ cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells302
"""
}
}
--
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