Configuration

Supported Config Styles

sRNA-IMP supports three configuration patterns: - single-sample YAML - multi-sample YAML with a samples: list - TSV-driven multi-sample mode with samples_tsv: in YAML

Shared Sections

Typical shared sections are: - project - settings - tools - workflows

Sample-specific Inputs

Per sample, the pipeline needs: - name - type - fastq - optional assembly_fasta - optional assembly_gff

Important Workflow Settings

preprocessing

• min_length
• max_length
• run_fastqc
• host_reference_fastas
• optional host_filter_indexes

host_specific

• mirna_index
• trna_index
• rrna_index
• other_ncrna_index

nonhost_specific

• kraken_db
• bracken_db
• trna_index
• mirna_euk_index
• rfam_class_index
• rfamseq_tsv

novel_ncrna

• min_length
• max_length
• min_reads
• merge_distance
• mismatches
• optional rfam_cm