diff --git a/workflow/conf/aws.config b/workflow/conf/aws.config
deleted file mode 100644
index 41585d2fb2e5d00895308a4c5b05811761947ae1..0000000000000000000000000000000000000000
--- a/workflow/conf/aws.config
+++ /dev/null
@@ -1,48 +0,0 @@
-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'
- }
-}
diff --git a/workflow/conf/bicf_logo.png b/workflow/conf/bicf_logo.png
deleted file mode 100644
index 0d8015590c5a94f92c39ec2470bd02baa3d09077..0000000000000000000000000000000000000000
Binary files a/workflow/conf/bicf_logo.png and /dev/null differ
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
deleted file mode 100644
index 983b458356f832bfe2cf0ce2ef2a5eeae919366c..0000000000000000000000000000000000000000
--- a/workflow/conf/biohpc.config
+++ /dev/null
@@ -1,73 +0,0 @@
-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'
-}
diff --git a/workflow/conf/cluster.config b/workflow/conf/cluster.config
deleted file mode 100644
index 4685e9b67c56ec662534a04bfc340b16fcd66873..0000000000000000000000000000000000000000
--- a/workflow/conf/cluster.config
+++ /dev/null
@@ -1,33 +0,0 @@
-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'
- }
-}
diff --git a/workflow/conf/local.config b/workflow/conf/local.config
deleted file mode 100755
index 9ca703b1d7f806b19fde6bd88a4fe2e7caeed1af..0000000000000000000000000000000000000000
--- a/workflow/conf/local.config
+++ /dev/null
@@ -1,3 +0,0 @@
-process {
- executor = 'local'
-}
\ No newline at end of file
diff --git a/workflow/conf/multiqc_config.yaml b/workflow/conf/multiqc_config.yaml
deleted file mode 100755
index 2ff18a76db2868839cc4789d94bc08fdfa5df70b..0000000000000000000000000000000000000000
--- a/workflow/conf/multiqc_config.yaml
+++ /dev/null
@@ -1,62 +0,0 @@
-# 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
diff --git a/workflow/configs/aws.config b/workflow/configs/aws.config
index 86a5b3187b7418a2bdc16c1c6cedb4473a204177..5e28c1edf8f29b7ab2d7554a8cc387e08699fb51 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/biohpc.config b/workflow/configs/biohpc.config
index 1da174a128ff30cb2a47790566792d5f4d267cee..983b458356f832bfe2cf0ce2ef2a5eeae919366c 100644
--- a/workflow/configs/biohpc.config
+++ b/workflow/configs/biohpc.config
@@ -1,6 +1,9 @@
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'
diff --git a/workflow/configs/cluster.config b/workflow/configs/cluster.config
index ed3da8d938bf96f44bb103ab83e75f4f9bbacd4b..77c404425eeef6abf8e9ff6e25f10145b4868783 100644
--- a/workflow/configs/cluster.config
+++ b/workflow/configs/cluster.config
@@ -1,27 +1,33 @@
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'
}
}
diff --git a/workflow/main.nf b/workflow/main.nf
index d727bb876521fc67bcd8c504c94f8b8af9308a8d..b186542a33ceab613434d0b6067d5b3b25d3fbdc 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") {
@@ -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
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index c402bf3f2ca76befef3ba984286493637520e3ad..1ab9a50bd365b61631b3df6441a59dd34480855b 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'