RNAchrom Configuration

The RNAchrom workflow uses a configuration file to specify various parameters and options. This document describes the key sections and parameters in the configuration file. We have provided a list of configurations most suitable for data processing of each experiment type. While core tools and parameters are constant across pipelines to ensure reliability, each configuration uniquely tailors settings to align with the specific analysis type. Those options are the ones used while preparing raw files for RNA-Chrom database.

The pipeline supports various all-to-all experiment types, each with its own configuration file. Click on the configuration file name to view more details.

iMARGI: iMARGI experiment configuration
GRID: GRID experiment configuration
CHAR-seq: CHAR-seq experiment configuration
Red-C: Red-C experiment configuration
Red-ChIP: Red-ChIP experiment configuration

These configs share a common structure but differ in key aspects:

Experiment type
Bridge processing settings and sequences
Alignment tools and parameters
Other specific flags for processing tools

Below you can explore options in details.

Input Options

Parameter	Description
`input`	Path to input file(s)
`exp_type`	Type of experiment (e.g. ‘grid’, ‘radicl’, ‘imargi’)
`procedure`	Processing procedure (‘old’ or ‘new’)
`split_by_chromosomes`	Whether to split processing by chromosomes (true/false)

Processing Tools

Those options determine which specific tools are used at each step of the workflow, affecting processing speed and output quality. All available tools from modules are listed below:

Parameter	Description
`dedup_tool`	Tool for deduplication (options: “fastq-dupaway”, “fastuniq”, “climpify”)
`trim_tool`	Tool for read trimming (options: “trimmomatic”, “bbduk”, “cutadapt”, “fastp”)
`align_tool`	Tool for alignment (options: “hisat2”, “bowtie2”, “star”)
`merge_pairedend_tool`	Tool for merging paired-end reads (options: “bbmerge”, “pear”)

Reference Genome

Parameter	Description
`genome`	Reference genome identifier (“GRCh38”, “GRCm38” “TAIR10”, … )
`genome_fasta`	Path to reference genome FASTA file
`hisat2_index`; `bwa_index`; `star_index`	Path to aligner index files
`splice_sites`	Path to splice sites file (optional)

Annotation Files

Parameter	Description
`annot_BED`	Path to BED annotation file
`annot_GTF`	Path to GTF annotation file
`blacklist`	Path to blacklist regions file
`chromsizes`	Path to chromosome sizes file
`detect_strand_genes_list`	Path to gene list for strand detection

Restriction Sites & Bridge Processing

Parameter	Description
`dna_part_processing`	Pattern for DNA part processing
`rna_part_processing`	Pattern for RNA part processing
`bridge_processing`	Enable bridge processing (true/false)
`debridge_tool`	Tool for debridge processing (options: “bitap”, “chartools”)
`forward_bridge_seq`	Forward bridge sequence
`reverse_bridge_seq`	Reverse bridge sequence
`max_mismatches`	Maximum allowed mismatches
`min_rna_dna_parts_length`	Minimum length of RNA/DNA parts
`description_sequence`	Description of sequence processing

Other Options

Parameter	Description
`smartseq_filter`	Enable Smart-seq filtering (true/false)
`max_memory`	Maximum memory allocation
`max_cpus`	Maximum CPU cores to use
`max_time`	Maximum run time
`outdir`	Output directory path
`publish_dir_mode`	Mode for publishing output files
`email`	Email for notifications

Command Flags

The configuration file includes specific flags for various tools:

fastq_dupaway: Flags for fastq-dupaway
trimmomatic: Flags for Trimmomatic
fastp: Flags for fastp
pear: Flags for PEAR
bam_filter: Flags for BAM filtering

Environment Variables

The config file also sets various environment variables like PYTHONPATH, R_PROFILE_USER, etc.

Included Configs

The main config file includes additional config files:

base.config: Base configuration for all pipelines
modules.config: DSL2 module specific options

This configuration setup allows flexible customization of the RNAchrom workflow for different experimental designs and processing requirements.