Commit 83890557 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Merge branch 'cellranger-4.0.0_ref-2020A' into '50-seurat.object'

Cellranger 4.0.0 ref 2020 a

See merge request !75
parents 60f343c4 26460c2c
Pipeline #7861 failed with stages
in 36 minutes and 24 seconds
workDir = 's3://'
aws.client.storageEncryption = 'AES256'
aws {
region = ''
batch {
cliPath = '/home/ec2-user/miniconda/bin/aws'
}
}
process {
executor = 'awsbatch'
queue = 'default-'
cpus = 1
memory = '1 GB'
withLabel: checkDesignFile {
cpus = 2
memory = '1 GB'
}
withLabel: count211 {
cpus = 2
memory = '30 GB'
}
withLabel: count220 {
cpus = 2
memory = '30 GB'
}
withLabel: count302 {
cpus = 2
memory = '30 GB'
}
withLabel: count310 {
cpus = 2
memory = '30 GB'
}
withLabel: count400 {
cpus = 2
memory = '30 GB'
}
withLabel: versions {
cpus = 3
memory = '1 GB'
}
withLabel: multiqc {
cpus = 1
memory = '1 GB'
}
}
params {
// Reference file paths on BioHPC
genomes {
'GRCh38-2020-A' {
loc = '/project/apps_database/cellranger/refdata-gex-'
}
'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-'
}
'mm10-2020-A' {
loc = '/project/apps_database/cellranger/refdata-gex-'
}
'mm10-3.0.0' {
loc = '/project/apps_database/cellranger/refdata-cellranger-'
}
'mm10-1.2.0' {
loc = '/project/apps_database/cellranger/refdata-cellranger-'
}
'GRCh38_and_mm10-2020-A' {
loc = '/project/apps_database/cellranger/refdata-gex-'
}
'GRCh38_and_mm10-3.1.0' {
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-'
}
}
// Chemistry mapping parameter
chemistry {
'auto' {
param = 'auto'
}
'3GEXv1' {
param = 'SC3Pv1'
}
'3GEXv2' {
param = 'SC3Pv2'
}
'3GEXv3' {
param = 'SC3Pv3'
}
'5GEX' {
param = 'fiveprime'
}
}
}
singularity {
enabled = true
cacheDir = '/project/BICF/BICF_Core/shared/gudmap/singularity_cache/'
}
env {
http_proxy = 'http://proxy.swmed.edu:3128'
https_proxy = 'http://proxy.swmed.edu:3128'
all_proxy = 'http://proxy.swmed.edu:3128'
}
process {
executor = 'slurm'
queue = '32GB'
clusterOptions = '--hold'
withLabel: trackStart {
executor = 'local'
}
withLabel: checkDesignFile {
executor = 'local'
}
withLabel: count211 {
queue = '128GB,256GB,256GBv1,384GB'
}
withLabel: count220 {
queue = '128GB,256GB,256GBv1,384GB'
}
withLabel: count302 {
queue = '128GB,256GB,256GBv1,384GB'
}
withLabel: count310 {
queue = '128GB,256GB,256GBv1,384GB'
}
withLabel: count400 {
queue = '128GB,256GB,256GBv1,384GB'
}
withLabel: versions {
executor = 'local'
}
withLabel: multiqc {
executor = 'local'
}
}
process {
executor = 'local'
}
\ No newline at end of file
# Custom Logo
custom_logo: 'bicf_logo.png'
custom_logo_url: 'https://www.utsouthwestern.edu/labs/bioinformatics/'
custom_logo_title: 'Bioinformatics Core Facility'
report_header_info:
- Contact E-mail: 'bicf@utsouthwestern.edu'
- Application Type: 'cellranger_count'
- Department: 'Bioinformatic Core Facility, Department of Bioinformatics'
# Title to use for the report.
title: BICF CellRanger Count Analysis Report
report_comment: >
This report has been generated by the <a href="https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count"
target="_blank">BICF/cellranger_count</a> pipeline.
custom_data:
metrics_summary:
file_format: 'tsv'
id: 'metrics_summary'
contents: 'Estimated Number of Cells Mean Reads per Cell Median Genes per Cell Number of Reads Valid Barcodes Sequencing Saturation Q30 Bases in Barcode Q30 Bases in RNA Read Q30 Bases in UMI Reads Mapped to Genome Reads Mapped Confidently to Genome Reads Mapped Confidently to Intergenic Regions Reads Mapped Confidently to Intronic Regions Reads Mapped Confidently to Exonic Regions Reads Mapped Confidently to Transcriptome Reads Mapped Antisense to Gene Fraction Reads in Cells Total Genes Detected Median UMI Counts per Cell'
section_name: 'Metrics Summary'
plot_type: 'generalstats'
sp:
metrics_summary:
fn: 'metrics_summary_mqc.tsv'
table_columns_placement:
metrics_summary:
Estimated Number of Cells: 1
Mean Reads per Cell: 2
Median Genes per Cell: 3
Number of Reads: 4
Sequencing Saturation: 5
Reads Mapped Confidently to Genome: 6
Reads Mapped Confidently to Transcriptome: 7
Fraction Reads in Cells: 8
Total Genes Detected: 9
Median UMI Counts per Cell: 10
Valid Barcodes: 1100
Reads Mapped Antisense to Gene: 1200
table_columns_visible:
metrics_summary:
Q30 Bases in Barcode: False
Q30 Bases in RNA Read: False
Q30 Bases in UMI: False
Reads Mapped to Genome: False
Reads Mapped Confidently to Intergenic Regions: False
Reads Mapped Confidently to Intronic Regions: False
Reads Mapped Confidently to Exonic Regions: False
thousandsSep_format: ''
report_section_order:
software_versions:
order: -1100
software_references:
order: -1200
......@@ -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'
}
......
params {
// Reference file paths on BioHPC
genomes {
'GRCh38-2020-A' {
loc = '/project/apps_database/cellranger/refdata-gex-'
}
'GRCh38-3.0.0' {
loc = '/project/apps_database/cellranger/refdata-cellranger-'
}
......@@ -13,12 +16,18 @@ params {
'hg19-1.2.0' {
loc = '/project/apps_database/cellranger/refdata-cellranger-'
}
'mm10-2020-A' {
loc = '/project/apps_database/cellranger/refdata-gex-'
}
'mm10-3.0.0' {
loc = '/project/apps_database/cellranger/refdata-cellranger-'
}
'mm10-1.2.0' {
loc = '/project/apps_database/cellranger/refdata-cellranger-'
}
'GRCh38_and_mm10-2020-A' {
loc = '/project/apps_database/cellranger/refdata-gex-'
}
'GRCh38_and_mm10-3.1.0' {
loc = '/project/apps_database/cellranger/refdata-cellranger-'
}
......@@ -52,6 +61,11 @@ params {
}
}
singularity {
enabled = true
cacheDir = '/project/BICF/BICF_Core/shared/gudmap/singularity_cache/'
}
env {
http_proxy = 'http://proxy.swmed.edu:3128'
https_proxy = 'http://proxy.swmed.edu:3128'
......
process {
executor = 'slurm'
queue = 'super'
queue = '32GB'
clusterOptions = '--hold'
withName:trackStart {
withName: trackStart {
executor = 'local'
}
withName:checkDesignFile {
withName: checkDesignFile {
executor = 'local'
}
withName:count211 {
withName: count211 {
queue = '128GB,256GB,256GBv1,384GB'
}
withName:count302 {
withName: count220 {
queue = '128GB,256GB,256GBv1,384GB'
}
withName:count310 {
withName: count302 {
queue = '128GB,256GB,256GBv1,384GB'
}
withName:versions {
withName: count310 {
queue = '128GB,256GB,256GBv1,384GB'
}
withName: count400 {
queue = '128GB,256GB,256GBv1,384GB'
}
withName: versions {
executor = 'local'
}
withName:multiqc {
withName: multiqc {
executor = 'local'
}
}
......@@ -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") {
......@@ -169,7 +172,7 @@ refLocation.into {
expectCells211 = expectCells
expectCells302 = expectCells
expectCells310 = expectCells
expectCells3400 = expectCells
expectCells400 = expectCells
forceCells211 = forceCells
forceCells302 = forceCells
forceCells310 = forceCells
......@@ -330,7 +333,7 @@ process count400 {
input:
set sample, file("${sample}_S?_L001_R1_001.fastq.gz"), file("${sample}_S?_L001_R2_001.fastq.gz"), file(script) from samples400
file ref from refLocation310.first()
file ref from refLocation400.first()
expectCells400
forceCells400
chemistryParam400
......
profiles {
standard {
includeConfig 'configs/biohpc.config'
includeConfig 'configs/cluster.config'
}
biohpc {
includeConfig 'configs/biohpc.config'
......
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