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/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..4685e9b67c56ec662534a04bfc340b16fcd66873 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 {
+ withLabel: trackStart {
executor = 'local'
}
- withName:checkDesignFile {
+ withLabel: checkDesignFile {
executor = 'local'
}
- withName:count211 {
+ withLabel: count211 {
queue = '128GB,256GB,256GBv1,384GB'
}
- withName:count302 {
+ withLabel: count220 {
queue = '128GB,256GB,256GBv1,384GB'
}
- withName:count310 {
+ withLabel: count302 {
queue = '128GB,256GB,256GBv1,384GB'
}
- withName:versions {
+ withLabel: count310 {
+ queue = '128GB,256GB,256GBv1,384GB'
+ }
+ withLabel: count400 {
+ queue = '128GB,256GB,256GBv1,384GB'
+ }
+ withLabel: versions {
executor = 'local'
}
- withName:multiqc {
+ withLabel: multiqc {
executor = 'local'
}
}