sqanti3_wrapper.conf

#!/bin/bash

# Conf for SQANTI3 wrapper
# Includes all variables needed to execute all optional parameters of SQANTI3_QC,
# SQANTI3_filter and SQANTI3_rescue.
# Using this wrapper helps to know the execution parameters of a run

sqanti3_qc="python3 sqanti3_qc.py"
sqanti3_filter="python3 sqanti3_filter.py"
sqanti3_rescue="python3 sqanti3_rescue.py"

# Somewhat common arguments for QC, Filter and rescue
# This parameters will (99.9% of the time) be common between the steps
# They only need to be defined once, and referenced within the script or conf
reference_gtf="example/gencode.v38.basic_chr22.gtf"
reference_fasta="example/GRCh38.p13_chr22.fasta"
cpus="4"
json_for_rules="utilities/filter/filter_default.json" # json file with rules for filter and rescue rules
threshold="0.7" 

# Execution control
# Skip parts at will, however, be careful if you skip QC or filter, but you
# need one of its ouput later and still does not exist, it will fail.

skip_qc="true" #true to skip the QC
skip_filter="true" # true to skip the filter
filter_mode="both" # rules, ml or both
skip_rescue="false" # true to skip the rescue
rescue_mode="both" # rules, ml or both

# Sqanti3.qc

QC_input="example/UHR_chr22.gtf" # Input data
QC_min_ref_length="" # minimum reference transcript length. Default 0 bp
QC_force_id_ignore="" 
QC_cage_peak_bed_file="data/ref_TSS_annotation/human.refTSS_v3.1.hg38.bed"
QC_aligner_choice="" # minimap2, deSALT, gmap or uLTRA
QC_polyA_motif_list="data/polyA_motifs/mouse_and_human.polyA_motif.txt"
QC_polyA_peak=""
QC_phylobed=""
QC_skipORF="true"
QC_is_fusion="false"
QC_orf_input=""
QC_is_fastq="false" # Requiered to be true if QC_input is a fastq file.
QC_expression_matrix=""
QC_gmap_index=""
QC_chunks=1
QC_output_prefix="UHR_chr22"
QC_destination_folder="/tmp/sqanti3_wrapper/QC/"
QC_coverage="" # Junctions coverage file
QC_sites=""
QC_window=""
QC_genename="" # Column name from GTF to define gene names
QC_full_length_pacbio_abundance_tsv="example/UHR_abundance.tsv"
QC_saturation="true"
QC_report_file="both" # pdf, html or both
QC_isoAnnotLite=""
QC_gff3=""
QC_short_reads_fofn="example/UHR_chr22_short_reads.fofn"
QC_SR_bam=""
QC_isoform_hits=""
QC_ratio_TSS_metric="" # Which metric should be reported in the ratio_TSS column



# Sqanti3.filter

# Common elements for filter rules and ml
filter_skip_report="false"
filter_input_classification="${QC_destination_folder}/${QC_output_prefix}_classification.txt" 
filter_corrected_gtf="${QC_destination_folder}/${QC_output_prefix}_corrected.gtf"
filter_isoforms="GMST/GMST_tmp.faa"
filter_isoannotgff3="example/SQANTI3_QC_output/UHR_chr22.gff3"
filter_sam=""
filter_faa="${QC_destination_folder}/${QC_output_prefix}_corrected.faa"
filter_monoexonic="true"
filter_skip_report=""

filter_cpus=${cpus}

# Filter rules parameters
filter_rules_ouput_folder="/tmp/sqanti3_wrapper/sqanti3_filter_rules"
filter_rules_prefix="${QC_output_prefix}"
filter_rules_json_file=${json_for_rules}

# Filter ml parameters
filter_ml_ouput_folder="/tmp/sqanti3_wrapper/sqanti3_filter_ml"
filter_ml_prefix="${QC_output_prefix}"
filter_ml_percent_training="0.8"
filter_ml_TP=""
filter_ml_TN=""
filter_ml_threshold=${threshold}
filter_ml_remove_columns=""
filter_ml_intermediate_files=""
filter_ml_max_class_size=""
filter_ml_intrapriming=""

# Sqanti3.rescue

# Rescue rules parameters
rescue_rules_filtered_classification="${filter_rules_ouput_folder}/${filter_rules_prefix}_RulesFilter_result_classification.txt"
rescue_rules_reference_classification="${QC_destination_folder}/${QC_output_prefix}_classification.txt"
rescue_rules_isoforms="${QC_destination_folder}/${QC_output_prefix}_corrected.fasta"
rescue_rules_gtf="${filter_rules_ouput_folder}/${filter_rules_prefix}.filtered.gtf"
rescue_rules_monoexons="all"
rescue_rules_mode="full"
rescue_rules_output_prefix="${QC_output_prefix}"
rescue_rules_output_folder="/tmp/sqanti3_wrapper/sqanti3_rescue_rules"


# Rescue ml parameters
rescue_ml_filtered_classification="${filter_ml_ouput_folder}/${filter_ml_prefix}_MLresult_classification.txt"
rescue_ml_reference_classification="${QC_destination_folder}/${QC_output_prefix}_classification.txt"
rescue_ml_isoforms="${QC_destination_folder}/${QC_output_prefix}_corrected.fasta"
rescue_ml_gtf="${filter_ml_ouput_folder}/${filter_ml_prefix}.filtered.gtf"
rescue_ml_monoexons="all"
rescue_ml_mode="full"
rescue_ml_output_prefix="${QC_output_prefix}"
rescue_ml_output_folder="/tmp/sqanti3_wrapper/sqanti3_rescue_ml"
rescue_ml_monoexons="all"
rescue_ml_mode="full"
rescue_ml_randomforest_rdata="${filter_ml_ouput_folder}/randomforest.RData"


# WARNING ZONE: By default the QC, filter and Rescue use the common 
# parameters for references and static files but they can be changed
# if needed (although you probably won't need to'). 

# QC warning zone
QC_reference_gtf=${reference_gtf}
QC_reference_fasta=${reference_fasta}
QC_cpus=${cpus}

# Rescue warning zone

rescue_rules_reference_genome=${reference_fasta}
rescue_rules_reference_gtf=${reference_gtf}
rescue_rules_json_file="${json_for_rules}"

rescue_ml_reference_genome=${reference_fasta}
rescue_ml_reference_gtf=${reference_gtf}
rescue_ml_threshold=${threshold}