Python library for running IGF pipelines
Sequencing run processing
Metadata registration
Monitor sequencing run for demultiplexing
Switch off project barcode checking
Accept modified samplesheet for demultiplexing run
Copy files to temp directory for demultiplexing run
Transfer metadata to experiment from sample entries
Pipeline control
Reset pipeline for data processing
Samplesheet processing
Divide samplesheet data
Reformat samplesheet for demultiplexing
Calculate basesmask for demultiplexing
Create or modify data to database
Clean up data from existing database and create new tables
Load flowcell runs to database
Load pipeline configuration to database
Load sequencing platform information to database
Load sequencing run information to database from a text input
Load file entries and build collection in database
Check Storage utilisation
Calculate disk usage summary
Calculate disk usage for a top level directory
Merge disk usage summary file and build a gviz json
Seed analysis pipeline
IGF database schema and api
Database schema
Database adaptor api
Base adaptor
Project adaptor
User adaptor
Sample adaptor
Experiment adaptor
Run adaptor
Collection adaptor
File adaptor
Sequencing run adaptor
Platform adaptor
Pipeline adaptor
Utility functions for database access
Database utility functions
Project adaptor utility functions
Sequencing adaptor utility functions
Pipeline adaptor utility functions
Platform adaptor utility functions
Pipeline seed adaptor utility functions
IGF pipeline api
Pipeline api
Fetch fastq files for analysis
Load analysis result to database and file system
Run metadata validation checks
Generic utility functions
Basic fasta sequence processing
Advanced fastq file processing
Process local and remote files
Load files to irods server
Calculate storage statistics
Run analysis tools
Process fastqc output file
Cellranger count utils
BWA utils
Picard utils
Fastp utils
GATK utils
RSEM utils
Samtools utils
STAR utils
Subread utils
Reference genome fetch utils
Samtools utils
Scanpy utils
Metadata processing
Register metadata for new projects
Update experiment metadata from sample attributes
Sequencing run
Process samplesheet file
Fetch read cycle info from RunInfo.xml file
Fetch flowcell info from runparameters xml file
Find and process new sequencing run for demultiplexing
Demultiplexing
Bases mask calculation
Copy bcl files for demultiplexing
Collect demultiplexed fastq files to database
Check demultiplexing barcode stats
Pipeline control
Reset pipeline seeds for re-processing
Reset samplesheet files after modification for rerunning pipeline
Demultiplexing of single cell sample
Modify samplesheet for singlecell samples
Merge fastq files for single cell samples
Report page building
Configure Biodalliance genome browser for qc page
Process Google chart json data
Generate data for QC project page
Generate data for QC status page
Generate data for QC analysis page
Python library for running IGF pipelines
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Python library for running IGF pipelines
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Python library for running IGF pipelines
List of python scripts
Sequencing run processing
Metadata registration
Monitor sequencing run for demultiplexing
Switch off project barcode checking
Accept modified samplesheet for demultiplexing run
Copy files to temp directory for demultiplexing run
Transfer metadata to experiment from sample entries
Pipeline control
Reset pipeline for data processing
Samplesheet processing
Divide samplesheet data
Reformat samplesheet for demultiplexing
Calculate basesmask for demultiplexing
Create or modify data to database
Clean up data from existing database and create new tables
Load flowcell runs to database
Load pipeline configuration to database
Load sequencing platform information to database
Load sequencing run information to database from a text input
Load file entries and build collection in database
Check Storage utilisation
Calculate disk usage summary
Calculate disk usage for a top level directory
Merge disk usage summary file and build a gviz json
Seed analysis pipeline
List of python classes and functions
IGF database schema and api
Database schema
Database adaptor api
Base adaptor
Project adaptor
User adaptor
Sample adaptor
Experiment adaptor
Run adaptor
Collection adaptor
File adaptor
Sequencing run adaptor
Platform adaptor
Pipeline adaptor
Utility functions for database access
Database utility functions
Project adaptor utility functions
Sequencing adaptor utility functions
Pipeline adaptor utility functions
Platform adaptor utility functions
Pipeline seed adaptor utility functions
IGF pipeline api
Pipeline api
Fetch fastq files for analysis
Load analysis result to database and file system
Run metadata validation checks
Generic utility functions
Basic fasta sequence processing
Advanced fastq file processing
Process local and remote files
Load files to irods server
Calculate storage statistics
Run analysis tools
Process fastqc output file
Cellranger count utils
BWA utils
Picard utils
Fastp utils
GATK utils
RSEM utils
Samtools utils
STAR utils
Subread utils
Reference genome fetch utils
Samtools utils
Scanpy utils
Metadata processing
Register metadata for new projects
Update experiment metadata from sample attributes
Sequencing run
Process samplesheet file
Fetch read cycle info from RunInfo.xml file
Fetch flowcell info from runparameters xml file
Find and process new sequencing run for demultiplexing
Demultiplexing
Bases mask calculation
Copy bcl files for demultiplexing
Collect demultiplexed fastq files to database
Check demultiplexing barcode stats
Pipeline control
Reset pipeline seeds for re-processing
Reset samplesheet files after modification for rerunning pipeline
Demultiplexing of single cell sample
Modify samplesheet for singlecell samples
Merge fastq files for single cell samples
Report page building
Configure Biodalliance genome browser for qc page
Process Google chart json data
Generate data for QC project page
Generate data for QC status page
Generate data for QC analysis page
Indices and tables
Index
Module Index
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