From 3bf035482ca03fe67b558a4ed722ebb65d8cf81b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 2 Mar 2021 15:54:13 -0600
Subject: [PATCH] Remove unnecessary configs
---
conf/.gitkeep | 0
conf/Execution_Run_For_Output_Bag.json | 64 -------
conf/Replicate_For_Input_Bag.json | 97 ----------
conf/aws.config | 135 -------------
conf/biohpc.config | 111 -----------
conf/biohpc_max.config | 16 --
conf/multiqc_config.yaml | 180 ------------------
conf/ondemand.config | 3 -
conf/spot.config | 3 -
.../Execution_Run_For_Output_Bag.json | 64 -------
nextflowConf/Replicate_For_Input_Bag.json | 97 ----------
nextflowConf/bdbag.json | 28 ---
12 files changed, 798 deletions(-)
delete mode 100644 conf/.gitkeep
delete mode 100755 conf/Execution_Run_For_Output_Bag.json
delete mode 100644 conf/Replicate_For_Input_Bag.json
delete mode 100644 conf/aws.config
delete mode 100755 conf/biohpc.config
delete mode 100755 conf/biohpc_max.config
delete mode 100644 conf/multiqc_config.yaml
delete mode 100755 conf/ondemand.config
delete mode 100755 conf/spot.config
delete mode 100755 nextflowConf/Execution_Run_For_Output_Bag.json
delete mode 100644 nextflowConf/Replicate_For_Input_Bag.json
delete mode 100644 nextflowConf/bdbag.json
diff --git a/conf/.gitkeep b/conf/.gitkeep
deleted file mode 100644
index e69de29..0000000
diff --git a/conf/Execution_Run_For_Output_Bag.json b/conf/Execution_Run_For_Output_Bag.json
deleted file mode 100755
index 5945b1e..0000000
--- a/conf/Execution_Run_For_Output_Bag.json
+++ /dev/null
@@ -1,64 +0,0 @@
-{
- "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
deleted file mode 100644
index 508a024..0000000
--- a/conf/Replicate_For_Input_Bag.json
+++ /dev/null
@@ -1,97 +0,0 @@
-{
- "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
deleted file mode 100644
index 7f6003c..0000000
--- a/conf/aws.config
+++ /dev/null
@@ -1,135 +0,0 @@
-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:getRefERCC {
- cpus = 1
- memory = '1 GB'
- }
- withName:getRef {
- cpus = 1
- memory = '1 GB'
- }
- withName:fastqc {
- cpus = 1
- memory = '1 GB'
- }
- withName:seqwho {
- cpus = 1
- memory = '1 GB'
- }
- withName:trimData {
- cpus = 20
- memory = '2 GB'
- }
- withName:downsampleData {
- cpus = 1
- memory = '1 GB'
- }
- withName:alignSampleDataERCC {
- cpus = 50
- memory = '5 GB'
- }
- withName:alignSampleData {
- cpus = 50
- memory = '5 GB'
- }
- withName:inferMetadata {
- cpus = 5
- memory = '1 GB'
- }
- withName:checkMetadata {
- 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: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
deleted file mode 100755
index dff28cb..0000000
--- a/conf/biohpc.config
+++ /dev/null
@@ -1,111 +0,0 @@
-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:getRefERCC {
- queue = 'super'
- }
- withName:getRef {
- queue = 'super'
- }
- withName:fastqc {
- queue = 'super'
- }
- withName:seqwho {
- executor = 'local'
- }
- withName:trimData {
- queue = 'super'
- }
- withName:downsampleData {
- executor = 'local'
- }
- withName:alignSampleDataERCC {
- queue = '128GB,256GB,256GBv1,384GB'
- }
- withName:alignSampleData {
- queue = '128GB,256GB,256GBv1,384GB'
- }
- withName:inferMetadata {
- queue = 'super'
- }
- withName:checkMetadata {
- executor = 'local'
- }
- withName:alignData {
- queue = '256GB,256GBv1'
- }
- withName:dedupData {
- queue = 'super'
- }
- withName:countData {
- queue = 'super'
- }
- withName:makeBigWig {
- 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
deleted file mode 100755
index 0e93ccf..0000000
--- a/conf/biohpc_max.config
+++ /dev/null
@@ -1,16 +0,0 @@
-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
deleted file mode 100644
index ed1375a..0000000
--- a/conf/multiqc_config.yaml
+++ /dev/null
@@ -1,180 +0,0 @@
-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
deleted file mode 100755
index 131fdbb..0000000
--- a/conf/ondemand.config
+++ /dev/null
@@ -1,3 +0,0 @@
-process {
- queue = 'highpriority-0ef8afb0-c7ad-11ea-b907-06c94a3c6390'
-}
diff --git a/conf/spot.config b/conf/spot.config
deleted file mode 100755
index d9c7a4c..0000000
--- a/conf/spot.config
+++ /dev/null
@@ -1,3 +0,0 @@
-process {
- queue = 'default-0ef8afb0-c7ad-11ea-b907-06c94a3c6390'
-}
diff --git a/nextflowConf/Execution_Run_For_Output_Bag.json b/nextflowConf/Execution_Run_For_Output_Bag.json
deleted file mode 100755
index 5945b1e..0000000
--- a/nextflowConf/Execution_Run_For_Output_Bag.json
+++ /dev/null
@@ -1,64 +0,0 @@
-{
- "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/nextflowConf/Replicate_For_Input_Bag.json b/nextflowConf/Replicate_For_Input_Bag.json
deleted file mode 100644
index 508a024..0000000
--- a/nextflowConf/Replicate_For_Input_Bag.json
+++ /dev/null
@@ -1,97 +0,0 @@
-{
- "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/nextflowConf/bdbag.json b/nextflowConf/bdbag.json
deleted file mode 100644
index 2c2ab24..0000000
--- a/nextflowConf/bdbag.json
+++ /dev/null
@@ -1,28 +0,0 @@
-{
- "fetch_config": {
- "http": {
- "http_cookies": {
- "file_names": [
- "*cookies.txt"
- ],
- "scan_for_cookie_files": true,
- "search_paths": [
- "."
- ],
- "search_paths_filter": "*cookies.txt"
- }
- },
- "https": {
- "http_cookies": {
- "file_names": [
- "*cookies.txt"
- ],
- "scan_for_cookie_files": true,
- "search_paths": [
- "."
- ],
- "search_paths_filter": "*cookies.txt"
- }
- }
- }
-}
--
GitLab