Parameters and config locations in the IRMA Code

[ajkarloss]

 1.   Take the whole parameter sets from the IRMA run 
 2.   And, find where (which part of the code in github) those values comes from
 In summary, If we want to build a module for blue-tongue virus in-house, what should we do?

[ajkarloss]

The main command and Paramters

IRMA FLU /opt/irida/data/sequence/21013/2/250905_NB552450.2025-07-2282-1-2_S39_R1_001.fastq /opt/irida/data/sequence/21014/2/250905_NB552450.2025-07-2282-1-2_S39_R2_001.fastq resultDir && python3 '/opt/galaxy/21.09/tools/irma/createMissingFiles.py'

default parameters

program_name PROGRAM Iterative Refinement Meta-Assembler (IRMA)
program_version VERSION 1.2.0
last_git_commit_hash LAST_COMMIT e72b7a9d51ab9ad023c6fe69f53dcc95aac92510
sample RUN resultDir
paired_end_reads PAIRED 1
data LEFT;RIGHT /opt/irida/data/sequence/21013/2/250905_NB552450.2025-07-2282-1-2_S39_R1_001.fastq;/opt/irida/data/sequence/21014/2/250905_NB552450.2025-07-2282-1-2_S39_R2_001.fastq
module_name MODULE FLU
module_param_call MODULE_CONFIG FLU
parameter_file_name PARAM_FILE_NAME FLU
parameter_file_version PARAM_FILE_VERSION 1.0
match_last_program MATCH_PROG BLAT (-oneOff=1 -minIdentity=80 -tileSize=10)
align_last_program ALIGN_PROG SAM
sort_last_program SORT_PROG BLAT
align_last_deletion_type DEL_TYPE DEL
assemble_last_program ASSEM_PROG SSW (-x 5 -m 2 -o 10 -e 1)
match_programs MATCH_PROGS BLAT
sort_programs SORT_PROGS BLAT
align_programs ALIGN_PROGS SAM
deletion_types DEL_TYPES
blat_identity BLAT_IDENTITY 80
minimum_blat_match_length MIN_BLAT_MATCH 0
profiles phmms /opt/galaxy/21.09/database/dependencies/_conda/envs/mulled-v1-128050d3545b50c1484deda3fb78dbbb1f39729a7e8bd946e0dc2c44f6b95bb7/bin/IRMA_RES/modules/FLU/profiles
do_not_merge_read_pairs NO_MERGE 0
starting_reference REF_SET /opt/galaxy/21.09/database/dependencies/_conda/envs/mulled-v1-128050d3545b50c1484deda3fb78dbbb1f39729a7e8bd946e0dc2c44f6b95bb7/bin/IRMA_RES/modules/FLU/reference/consensus.fasta
grid_acceleration_on GRID_ON 0
grid_optional_path GRID_PATH "0"
working_directory ppath "/tmp/galaxy/IRMAv1.2.0/resultDir-AM5Z6cbpHAzfIc4dUUaekTQckuq8li3C"
alternative_frequency MIN_FA 1
alternative_count MIN_CA 20
skip_reference_elongation SKIP_E 1
read_statistic USE_MEDIAN 1
minimum_statistic_quality QUAL_THRESHOLD 30
minimum_read_length MIN_LEN 125
adapter_trim_read_motif ADAPTER AGATGTGTATAAGAGACAG
adapter_allow_one_mismatch FUZZY_ADAPTER 1
enforce_clipped_length ENFORCE_CLIPPED_LENGTH 0
interval_significance_level SIG_LEVEL 0.999
maximum_read_gathering_rounds MAX_ROUNDS 5
minimum_read_patterns MIN_RP 1
minimum_read_patterns_residual MIN_RP_RESIDUAL 150
minimum_reads MIN_RC 1
minimum_reads_residual MIN_RC_RESIDUAL 150
match_to_altmatch_ratio RESIDUAL_ASSEMBLY_FACTOR 0
minimum_insertion_edit_threshold INS_T 0.25
minimum_deletion_edit_threshold DEL_T 0.60
minimum_insertion_edit_depth INS_T_DEPTH 1
minimum_deletion_edit_depth DEL_T_DEPTH 1
silence_complex_indels_for_editing SILENCE_COMPLEX_INDELS 0
minimum_frequency_for_mixed_consensus_call MIN_AMBIG 0.20
minimum_consensus_support MIN_CONS_SUPPORT 1
minimum_consensus_average_quality MIN_CONS_QUALITY 0
minimum_amplicon_dropout_edge_depth MIN_DROPOUT_EDGE_DEPTH 0
auto_adjust_minimum_variant_frequency AUTO_F 1
minimum_deletion_variant_frequency MIN_FD 0.005
minimum_insertion_variant_frequency MIN_FI 0.005
minimum_variant_frequency MIN_F 0.008
minimum_variant_count MIN_C 2
minimum_variant_average_quality MIN_AQ 24
minimum_variant_depth MIN_TCC 100
minimum_confidence_not_sequencer_error MIN_CONF 0.80
merge_secondary_data MERGE_SECONDARY 0
do_secondary_assembly DO_SECONDARY 0
final_assembly_to_reference_seed ASSEM_REF 0
packaged_final_fastq PACKAGED_FASTQ 1
use_irma_core USE_IRMA_CORE 0