Pipeliner Documenation

• Requirements
  • Testing Nextflow
  • Installing Anaconda
  • Pre-Packaged Conda Environment
    • Yaml File
  • Setting up Pipeliner
• Basic Usage
  • Framework Stucture
  • Pipeline Configuration
    • Config Inheritance
    • Data Input and Output
    • Basic Options
    • Providing an Index
    • Starting from Bams
    • Temporary Files
    • Skipping Steps
  • Process Configuration
    • Descriptive Arguments
    • Xargs
    • Ainj
  • Pipeline Execution
  • Output and Results
    • Sample Folders
    • Expression Matrix
    • Bam Files
    • Alignment Index
    • Reports
• Pipeline Structure
  • Configuration File
    • File Paths
    • Executor and Compute Resources
    • Pipeline Options and Parameters
  • Pipeline Script
  • Template Processes
  • Output
• Existing Pipelines
  • RNA-seq
    • Check Reads check_reads
    • Genome Indexing hisat_indexing/star_indexing
    • Pre-Quality Check pre_fastqc
    • Pre-MultiQC pre_multiqc
    • Read Trimming trim_galore
    • Read Mapping hisat_mapping/star_mapping
    • Reformat Reference gtftobed
    • Mapping Quality rseqc
    • Quantification counting
    • Expression Matrix expression_matrix
    • Expression Features expression_features
    • Expression Set expression_set
    • Summary Report multiqc
  • scRNA-seq
    • Check Reads check_reads
    • Genome Indexing hisat_indexing/star_indexing
    • Quality Check fastqc
    • Whitelist whitelist
    • Extract extract
    • Read Mapping hisat_mapping/star_mapping
    • Reformat Reference gtftobed
    • Mapping Quality rseqc
    • Quantification counting
    • Summary Report multiqc
  • DGE
    • Quantification counting
    • Expression Matrix expression_matrix
    • Sample Renaming rename_samples
    • Summary Report multiqc
• Extending Pipelines
  • General Workflow
  • Configuration Inheritance
  • Template Process Injections
  • Testing Module