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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© Copyright 2018, Avik Datta, IGF Team. Revision 0b702a42.

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