diff --git a/conf/.gitkeep b/conf/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/conf/Execution_Run_For_Output_Bag.json b/conf/Execution_Run_For_Output_Bag.json
new file mode 100755
index 0000000000000000000000000000000000000000..5945b1eb8c4c5e3ec862840f232ed7a8e386d770
--- /dev/null
+++ b/conf/Execution_Run_For_Output_Bag.json
@@ -0,0 +1,64 @@
+{
+ "bag": {
+ "bag_name": "Execution_Run_{rid}",
+ "bag_algorithms": [
+ "md5"
+ ],
+ "bag_archiver": "zip",
+ "bag_metadata": {}
+ },
+ "catalog": {
+ "catalog_id": "2",
+ "query_processors": [
+ {
+ "processor": "csv",
+ "processor_params": {
+ "output_path": "Execution_Run",
+ "query_path": "/attribute/M:=RNASeq:Execution_Run/RID=17-BPAG/RID,Replicate_RID:=Replicate,Workflow_RID:=Workflow,Reference_Genone_RID:=Reference_Genome,Input_Bag_RID:=Input_Bag,Notes,Execution_Status,Execution_Status_Detail,RCT,RMT?limit=none"
+ }
+ },
+ {
+ "processor": "csv",
+ "processor_params": {
+ "output_path": "Workflow",
+ "query_path": "/entity/M:=RNASeq:Execution_Run/RID=17-BPAG/RNASeq:Workflow?limit=none"
+ }
+ },
+ {
+ "processor": "csv",
+ "processor_params": {
+ "output_path": "Reference_Genome",
+ "query_path": "/entity/M:=RNASeq:Execution_Run/RID=17-BPAG/RNASeq:Reference_Genome?limit=none"
+ }
+ },
+ {
+ "processor": "csv",
+ "processor_params": {
+ "output_path": "Input_Bag",
+ "query_path": "/entity/M:=RNASeq:Execution_Run/RID=17-BPAG/RNASeq:Input_Bag?limit=none"
+ }
+ },
+ {
+ "processor": "csv",
+ "processor_params": {
+ "output_path": "mRNA_QC",
+ "query_path": "/attribute/M:=RNASeq:Execution_Run/RID=17-BPAG/(RID)=(RNASeq:mRNA_QC:Execution_Run)/RID,Execution_Run_RID:=Execution_Run,Replicate_RID:=Replicate,Paired_End,Strandedness,Median_Read_Length,Raw_Count,Final_Count,Notes,RCT,RMT?limit=none"
+ }
+ },
+ {
+ "processor": "fetch",
+ "processor_params": {
+ "output_path": "assets/Study/{Study_RID}/Experiment/{Experiment_RID}/Replicate/{Replicate_RID}/Execution_Run/{Execution_Run_RID}/Output_Files",
+ "query_path": "/attribute/M:=RNASeq:Execution_Run/RID=17-BPAG/R:=RNASeq:Replicate/$M/(RID)=(RNASeq:Processed_File:Execution_Run)/url:=File_URL,length:=File_Bytes,filename:=File_Name,md5:=File_MD5,Execution_Run_RID:=M:RID,Study_RID:=R:Study_RID,Experiment_RID:=R:Experiment_RID,Replicate_RID:=R:RID?limit=none"
+ }
+ },
+ {
+ "processor": "fetch",
+ "processor_params": {
+ "output_path": "assets/Study/{Study_RID}/Experiment/{Experiment_RID}/Replicate/{Replicate_RID}/Execution_Run/{Execution_Run_RID}/Input_Bag",
+ "query_path": "/attribute/M:=RNASeq:Execution_Run/RID=17-BPAG/R:=RNASeq:Replicate/$M/RNASeq:Input_Bag/url:=File_URL,length:=File_Bytes,filename:=File_Name,md5:=File_MD5,Execution_Run_RID:=M:RID,Study_RID:=R:Study_RID,Experiment_RID:=R:Experiment_RID,Replicate_RID:=R:RID?limit=none"
+ }
+ }
+ ]
+ }
+}
\ No newline at end of file
diff --git a/conf/Replicate_For_Input_Bag.json b/conf/Replicate_For_Input_Bag.json
new file mode 100644
index 0000000000000000000000000000000000000000..508a0245051534fae39020792719b04d78947613
--- /dev/null
+++ b/conf/Replicate_For_Input_Bag.json
@@ -0,0 +1,97 @@
+{
+ "bag": {
+ "bag_name": "{rid}_inputBag",
+ "bag_algorithms": [
+ "md5"
+ ],
+ "bag_archiver": "zip"
+ },
+ "catalog": {
+ "query_processors": [
+ {
+ "processor": "csv",
+ "processor_params": {
+ "output_path": "Study",
+ "query_path": "/attribute/M:=RNASeq:Replicate/RID={rid}/(Study_RID)=(RNASeq:Study:RID)/Study_RID:=RID,Internal_ID,Title,Summary,Overall_Design,GEO_Series_Accession_ID,GEO_Platform_Accession_ID,Funding,Pubmed_ID,Principal_Investigator,Consortium,Release_Date,RCT,RMT?limit=none"
+ }
+ },
+ {
+ "processor": "csv",
+ "processor_params": {
+ "output_path": "Experiment",
+ "query_path": "/attribute/M:=RNASeq:Replicate/RID={rid}/(Experiment_RID)=(RNASeq:Experiment:RID)/Experiment_RID:=RID,Study_RID,Internal_ID,Name,Description,Experiment_Method,Experiment_Type,Species,Specimen_Type,Molecule_Type,Pooled_Sample,Pool_Size,Markers,Cell_Count,Treatment_Protocol,Treatment_Protocol_Reference,Isolation_Protocol,Isolation_Protocol_Reference,Growth_Protocol,Growth_Protocol_Reference,Label_Protocol,Label_Protocol_Reference,Hybridization_Protocol,Hybridization_Protocol_Reference,Scan_Protocol,Scan_Protocol_Reference,Data_Processing,Value_Definition,Notes,Principal_Investigator,Consortium,Release_Date,RCT,RMT?limit=none"
+ }
+ },
+ {
+ "processor": "csv",
+ "processor_params": {
+ "output_path": "Experiment Antibodies",
+ "query_path": "/entity/M:=RNASeq:Replicate/RID={rid}/(Experiment_RID)=(RNASeq:Experiment_Antibodies:Experiment_RID)?limit=none"
+ }
+ },
+ {
+ "processor": "csv",
+ "processor_params": {
+ "output_path": "Experiment Custom Metadata",
+ "query_path": "/entity/M:=RNASeq:Replicate/RID={rid}/(Experiment_RID)=(RNASeq:Experiment_Custom_Metadata:Experiment_RID)?limit=none"
+ }
+ },
+ {
+ "processor": "csv",
+ "processor_params": {
+ "output_path": "Experiment Settings",
+ "query_path": "/attribute/M:=RNASeq:Replicate/RID={rid}/(Experiment_RID)=(RNASeq:Experiment_Settings:Experiment_RID)/RID,Experiment_RID,Alignment_Format,Aligner,Aligner_Version,Reference_Genome,Sequence_Trimming,Duplicate_Removal,Pre-alignment_Sequence_Removal,Junction_Reads,Library_Type,Protocol_Reference,Library_Selection,Quantification_Format,Quantification_Software,Expression_Metric,Transcriptome_Model,Sequencing_Platform,Paired_End,Read_Length,Strandedness,Used_Spike_Ins,Spike_Ins_Amount,Visualization_Format,Visualization_Software,Visualization_Version,Visualization_Setting,Notes,RCT,RMT?limit=none"
+ }
+ },
+ {
+ "processor": "csv",
+ "processor_params": {
+ "output_path": "Replicate",
+ "query_path": "/attribute/M:=RNASeq:Replicate/RID={rid}/RID,Study_RID,Experiment_RID,Biological_Replicate_Number,Technical_Replicate_Number,Specimen_RID,Collection_Date,Mapped_Reads,GEO_Sample_Accession_ID,Notes,Principal_Investigator,Consortium,Release_Date,RCT,RMT?limit=none"
+ }
+ },
+ {
+ "processor": "csv",
+ "processor_params": {
+ "output_path": "Specimen",
+ "query_path": "/attribute/M:=RNASeq:Replicate/RID={rid}/S:=(Specimen_RID)=(Gene_Expression:Specimen:RID)/T:=left(Stage_ID)=(Vocabulary:Developmental_Stage:ID)/$S/RID,Title,Species,Stage_ID,Stage_Name:=T:Name,Stage_Detail,Assay_Type,Strain,Wild_Type,Sex,Passage,Phenotype,Cell_Line,Parent_Specimen,Upload_Notes,Preparation,Fixation,Embedding,Internal_ID,Principal_Investigator,Consortium,Release_Date,RCT,RMT,GUDMAP2_Accession_ID?limit=none"
+ }
+ },
+ {
+ "processor": "csv",
+ "processor_params": {
+ "output_path": "Specimen_Anatomical_Source",
+ "query_path": "/attribute/M:=RNASeq:Replicate/RID={rid}/(Specimen_RID)=(Gene_Expression:Specimen:RID)/(RID)=(Gene_Expression:Specimen_Tissue:Specimen_RID)/RID,Specimen_RID,Tissue,RCT,RMT?limit=none"
+ }
+ },
+ {
+ "processor": "csv",
+ "processor_params": {
+ "output_path": "Specimen_Cell_Types",
+ "query_path": "/attribute/M:=RNASeq:Replicate/RID={rid}/(Specimen_RID)=(Gene_Expression:Specimen:RID)/(RID)=(Gene_Expression:Specimen_Cell_Type:Specimen)/RID,Specimen_RID:=Specimen,Cell_Type,RCT,RMT?limit=none"
+ }
+ },
+ {
+ "processor": "csv",
+ "processor_params": {
+ "output_path": "Single Cell Metrics",
+ "query_path": "/attribute/M:=RNASeq:Replicate/RID={rid}/(RID)=(RNASeq:Single_Cell_Metrics:Replicate_RID)/RID,Study_RID,Experiment_RID,Replicate_RID,Reads_%28Millions%29,Reads%2FCell,Detected_Gene_Count,Genes%2FCell,UMI%2FCell,Estimated_Cell_Count,Principal_Investigator,Consortium,Release_Date,RCT,RMT?limit=none"
+ }
+ },
+ {
+ "processor": "csv",
+ "processor_params": {
+ "output_path": "File",
+ "query_path": "/attribute/M:=RNASeq:Replicate/RID={rid}/(RID)=(RNASeq:File:Replicate_RID)/RID,Study_RID,Experiment_RID,Replicate_RID,Caption,File_Type,File_Name,URI,File_size,MD5,GEO_Archival_URL,dbGaP_Accession_ID,Processed,Notes,Principal_Investigator,Consortium,Release_Date,RCT,RMT,Legacy_File_RID,GUDMAP_NGF_OID,GUDMAP_NGS_OID?limit=none"
+ }
+ },
+ {
+ "processor": "fetch",
+ "processor_params": {
+ "output_path": "assets/Study/{Study_RID}/Experiment/{Experiment_RID}/Replicate/{Replicate_RID}",
+ "query_path": "/attribute/M:=RNASeq:Replicate/RID={rid}/(RID)=(RNASeq:File:Replicate_RID)/File_Type=FastQ/File_Name::ciregexp::%5B_.%5DR%5B12%5D%5C.fastq%5C.gz/url:=URI,length:=File_size,filename:=File_Name,md5:=MD5,Study_RID,Experiment_RID,Replicate_RID?limit=none"
+ }
+ }
+ ]
+ }
+}
diff --git a/conf/aws.config b/conf/aws.config
new file mode 100644
index 0000000000000000000000000000000000000000..bf5b59c7cf9db00606a5db9f97c706d53f21137f
--- /dev/null
+++ b/conf/aws.config
@@ -0,0 +1,127 @@
+params {
+ refSource = "aws"
+}
+
+workDir = 's3://gudmap-rbk.output/work'
+aws.client.storageEncryption = 'AES256'
+aws {
+ region = 'us-east-2'
+ batch {
+ cliPath = '/home/ec2-user/miniconda/bin/aws'
+ }
+}
+
+process {
+ executor = 'awsbatch'
+ cpus = 1
+ memory = '1 GB'
+
+ withName:trackStart {
+ cpus = 1
+ memory = '1 GB'
+ }
+ withName:getBag {
+ cpus = 1
+ memory = '1 GB'
+ }
+ withName:getData {
+ cpus = 1
+ memory = '1 GB'
+ }
+ withName:parseMetadata {
+ cpus = 15
+ memory = '1 GB'
+ }
+ withName:trimData {
+ cpus = 20
+ memory = '2 GB'
+ }
+ withName:getRefInfer {
+ cpus = 1
+ memory = '1 GB'
+ }
+ withName:downsampleData {
+ cpus = 1
+ memory = '1 GB'
+ }
+ withName:alignSampleData {
+ cpus = 50
+ memory = '5 GB'
+ }
+ withName:inferMetadata {
+ cpus = 5
+ memory = '1 GB'
+ }
+ withName:checkMetadata {
+ cpus = 1
+ memory = '1 GB'
+ }
+ withName:getRef {
+ cpus = 1
+ memory = '1 GB'
+ }
+ withName:alignData {
+ cpus = 50
+ memory = '10 GB'
+ }
+ withName:dedupData {
+ cpus = 5
+ memory = '20 GB'
+ }
+ withName:countData {
+ cpus = 2
+ memory = '5 GB'
+ }
+ withName:makeBigWig {
+ cpus = 15
+ memory = '5 GB'
+ }
+ withName:fastqc {
+ cpus = 1
+ memory = '1 GB'
+ }
+ withName:dataQC {
+ cpus = 15
+ memory = '2 GB'
+ }
+ withName:aggrQC {
+ cpus = 2
+ memory = '1 GB'
+ }
+ withName:uploadInputBag {
+ cpus = 1
+ memory = '1 GB'
+ }
+ withName:uploadExecutionRun {
+ cpus = 1
+ memory = '1 GB'
+ }
+ withName:uploadQC {
+ cpus = 1
+ memory = '1 GB'
+ }
+ withName:uploadProcessedFile {
+ cpus = 1
+ memory = '1 GB'
+ }
+ withName:uploadOutputBag {
+ cpus = 1
+ memory = '1 GB'
+ }
+ withName:finalizeExecutionRun {
+ cpus = 1
+ memory = '1 GB'
+ }
+ withName:failPreExecutionRun {
+ cpus = 1
+ memory = '1 GB'
+ }
+ withName:failExecutionRun {
+ cpus = 1
+ memory = '1 GB'
+ }
+ withName:uploadQC_fail {
+ cpus = 1
+ memory = '1 GB'
+ }
+}
diff --git a/conf/biohpc.config b/conf/biohpc.config
new file mode 100755
index 0000000000000000000000000000000000000000..a12f2a704b3c63df9031789c2bb05d11e04d6b3a
--- /dev/null
+++ b/conf/biohpc.config
@@ -0,0 +1,105 @@
+params {
+ refSource = "biohpc"
+}
+
+process {
+ executor = 'slurm'
+ queue = 'super'
+ clusterOptions = '--hold'
+ time = '4h'
+ errorStrategy = 'retry'
+ maxRetries = 1
+
+ withName:trackStart {
+ executor = 'local'
+ }
+ withName:getBag {
+ executor = 'local'
+ }
+ withName:getData {
+ queue = 'super'
+ }
+ withName:parseMetadata {
+ executor = 'local'
+ }
+ withName:trimData {
+ queue = 'super'
+ }
+ withName:getRefInfer {
+ queue = 'super'
+ }
+ withName:downsampleData {
+ executor = 'local'
+ }
+ withName:alignSampleData {
+ queue = '128GB,256GB,256GBv1,384GB'
+ }
+ withName:inferMetadata {
+ queue = 'super'
+ }
+ withName:checkMetadata {
+ executor = 'local'
+ }
+ withName:getRef {
+ queue = 'super'
+ }
+ withName:alignData {
+ queue = '256GB,256GBv1'
+ }
+ withName:dedupData {
+ queue = 'super'
+ }
+ withName:countData {
+ queue = 'super'
+ }
+ withName:makeBigWig {
+ queue = 'super'
+ }
+ withName:fastqc {
+ queue = 'super'
+ }
+ withName:dataQC {
+ queue = 'super'
+ }
+ withName:aggrQC {
+ executor = 'local'
+ }
+ withName:uploadInputBag {
+ executor = 'local'
+ }
+ withName:uploadExecutionRun {
+ executor = 'local'
+ }
+ withName:uploadQC {
+ executor = 'local'
+ }
+ withName:uploadProcessedFile {
+ executor = 'local'
+ }
+ withName:uploadOutputBag {
+ executor = 'local'
+ }
+ withName:finalizeExecutionRun {
+ executor = 'local'
+ }
+ withName:failPreExecutionRun {
+ executor = 'local'
+ }
+ withName:failExecutionRun {
+ executor = 'local'
+ }
+ withName:uploadQC_fail {
+ executor = 'local'
+ }
+}
+
+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/conf/biohpc_max.config b/conf/biohpc_max.config
new file mode 100755
index 0000000000000000000000000000000000000000..0e93ccf6a0be4c15c076ab6eb955a4bb39d96120
--- /dev/null
+++ b/conf/biohpc_max.config
@@ -0,0 +1,16 @@
+process {
+ executor = 'slurm'
+ queue = '256GB,256GBv1,384GB,128GB'
+ clusterOptions = '--hold'
+}
+
+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/conf/multiqc_config.yaml b/conf/multiqc_config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..ed1375aed47a454394029e5057695b0c15babd8c
--- /dev/null
+++ b/conf/multiqc_config.yaml
@@ -0,0 +1,180 @@
+custom_logo: './bicf_logo.png'
+custom_logo_url: 'https/utsouthwestern.edu/labs/bioinformatics/'
+custom_logo_title: 'Bioinformatics Core Facility'
+
+report_header_info:
+ - Contact Email: 'bicf@utsouthwestern.edu'
+ - Application Type: 'RNA-Seq Analytic Pipeline for GUDMAP/RBK'
+ - Department: 'Bioinformatic Core Facility, Department of Bioinformatics, University of Texas Southwestern Medical Center'
+
+title: RNA-Seq Analytic Pipeline for GUDMAP/RBK
+
+report_comment: >
+ This report has been generated by the <a href="https://doi.org/10.5281/zenodo.3625056">GUDMAP/RBK RNA-Seq Pipeline</a>
+
+top_modules:
+ - fastqc:
+ name: 'Raw'
+ info: 'Replicate Raw fastq QC Results'
+ - cutadapt:
+ name: 'Trim'
+ info: 'Replicate Trim Adapter QC Results'
+ - hisat2:
+ name: 'Align'
+ info: 'Replicate Alignment QC Results'
+ path_filters:
+ - '*alignSummary*'
+ - picard:
+ name: 'Dedup'
+ info: 'Replicate Alignement Deduplication QC Results'
+ - rseqc:
+ name: 'Inner Distance'
+ info: 'Replicate Paired End Inner Distance Distribution Results'
+ path_filters:
+ - '*insertSize*'
+ - custom_content
+ - featureCounts:
+ name: 'Count'
+ info: 'Replicate Feature Count QC Results'
+ - hisat2:
+ name: 'Inference: Align'
+ info: 'Inference Alignment (1M downsampled reads) QC Results'
+ path_filters:
+ - '*alignSampleSummary*'
+ - rseqc:
+ name: 'Inference: Stranded'
+ info: '1M Downsampled Reads Strandedness Inference Results'
+ path_filters:
+ - '*infer_experiment*'
+
+report_section_order:
+ run:
+ order: 4000
+ rid:
+ order: 3000
+ meta:
+ order: 2000
+ ref:
+ order: 1000
+ software_versions:
+ order: -1000
+ software_references:
+ order: -2000
+
+skip_generalstats: true
+
+custom_data:
+ run:
+ file_format: 'tsv'
+ section_name: 'Run'
+ description: 'This is the run information'
+ plot_type: 'table'
+ pconfig:
+ id: 'run'
+ scale: false
+ format: '{}'
+ headers:
+ Session:
+ description: ''
+ Session ID:
+ description: 'Nextflow session ID'
+ Pipeline Version:
+ description: 'BICF pipeline version'
+ Input:
+ description: 'Input overrides'
+ rid:
+ file_format: 'tsv'
+ section_name: 'RID'
+ description: 'This is the identifying RIDs'
+ plot_type: 'table'
+ pconfig:
+ id: 'rid'
+ scale: false
+ format: '{}'
+ headers:
+ Replicate:
+ description: ''
+ Replicate RID:
+ description: 'Replicate RID'
+ Experiment RID:
+ description: 'Experiment RID'
+ Study RID:
+ description: 'Study RID'
+ meta:
+ file_format: 'tsv'
+ section_name: 'Metadata'
+ description: 'This is the comparison of infered metadata, submitter provided, and calculated'
+ plot_type: 'table'
+ pconfig:
+ id: 'meta'
+ scale: false
+ format: '{:,.0f}'
+ headers:
+ Source:
+ description: 'Metadata source'
+ Species:
+ description: 'Species'
+ Ends:
+ description: 'Single or paired end sequencing'
+ Stranded:
+ description: 'Stranded (forward/reverse) or unstranded library prep'
+ Spike-in:
+ description: 'ERCC spike in'
+ Raw Reads:
+ description: 'Number of reads of the sequencer'
+ Assigned Reads:
+ description: 'Final reads after fintering'
+ Median Read Length:
+ description: 'Average read length'
+ Median TIN:
+ description: 'Average transcript integrity number'
+
+ ref:
+ file_format: 'tsv'
+ section_name: 'Reference'
+ description: 'This is the reference version information'
+ plot_type: 'table'
+ pconfig:
+ id: 'ref'
+ scale: false
+ format: '{}'
+ headers:
+ Species:
+ description: 'Reference species'
+ Genome Reference Consortium Build:
+ description: 'Reference source build'
+ Genome Reference Consortium Patch:
+ description: 'Reference source patch version'
+ GENCODE Annotation Release:
+ description: 'Annotation release version'
+ tin:
+ file_format: 'tsv'
+ section_name: 'TIN'
+ description: 'This is the distribution of TIN values calculated by the tool RSeQC'
+ plot_type: 'bargraph'
+ pconfig:
+ id: 'tin'
+ headers:
+ chrom
+ 1 - 10
+ 11 - 20
+ 21 - 30
+ 31 - 40
+ 41 - 50
+ 51 - 60
+ 61 - 70
+ 71 - 80
+ 81 - 90
+ 91 - 100
+
+sp:
+ run:
+ fn: "run.tsv"
+ rid:
+ fn: 'rid.tsv'
+ meta:
+ fn: 'metadata.tsv'
+ ref:
+ fn: 'reference.tsv'
+ tin:
+ fn: '*_tin.hist.tsv'
diff --git a/conf/ondemand.config b/conf/ondemand.config
new file mode 100755
index 0000000000000000000000000000000000000000..131fdbb19e1fedf1bc9e206a03d801f13791b810
--- /dev/null
+++ b/conf/ondemand.config
@@ -0,0 +1,3 @@
+process {
+ queue = 'highpriority-0ef8afb0-c7ad-11ea-b907-06c94a3c6390'
+}
diff --git a/conf/spot.config b/conf/spot.config
new file mode 100755
index 0000000000000000000000000000000000000000..d9c7a4c8fa34aadd597da0170f8e3e223923011a
--- /dev/null
+++ b/conf/spot.config
@@ -0,0 +1,3 @@
+process {
+ queue = 'default-0ef8afb0-c7ad-11ea-b907-06c94a3c6390'
+}