config_SIRV.yml

---
## General pipeline parameters:

# Name of the pipeline:
pipeline: "pipeline-pinfish-analysis_sirv"
# ABSOLUTE path to directory holding the working directory:
workdir_top: "Workspaces"
# Repository URL:
repo: "https://github.com/nanoporetech/pipeline-pinfish-analysis.git"

## Pipeline-specific parameters:

threads: 50

# Input genome:
genome_fasta: "SIRV_150601a.fasta"

# CDNA or direct RNA reads in fastq format:
reads_fastq: "sirv_E0.fq"

# Extra option passed to minimap2 when generating index:
minimap_index_opts: "-k14"

# Extra options passed to minimap2:
#minimap2_opts: ""
# Enable this for stranded data:
minimap2_opts: "-uf --splice-flank=no --end-seed-pen 0"
# Enable this for SIRV data:
#minimap2_opts: "--splice-flank=no"

# Minmum mapping quality:
minimum_mapping_quality: 10

# Options passed to spliced_bam2gff:
#spliced_bam2gff_opts: ""
# Enable this for stranded data:
spliced_bam2gff_opts: "-s"

# -c parameter:
minimum_cluster_size: 40

# -p parameter:
minimum_isoform_percent: 0.3

# -d parameter:
exon_boundary_tolerance: 10

# -e parameter:
terminal_exon_boundary_tolerance: 30

# Extra options passed to minimap2 when mapping polished reads:
#minimap2_opts_polished: ""
# Enable this for stranded data:
minimap2_opts_polished: "-uf --splice-flank=no --end-seed-pen 0"
# Enable this for SIRV data:
#minimap2_opts_polished: "--splice-flank=no"

# Options passed to spliced_bam2gff when converting alignments of polished reads:
#spliced_bam2gff_opts_pol: ""
# Enable this for stranded data:
spliced_bam2gff_opts_pol: "-s"

# Options passed to collapse_partials when collapsing fragmentation artifacts
# in clustered and polished transcripts.

# Internal exon boundary tolerance:
collapse_internal_tol: 5

# Five prime boundary tolerance:
collapse_five_tol: 5000

# Three prime boundary tolerance:
collapse_three_tol: 30