defaults.yaml

#this file contains default values for the pipeline

# global nextflow parameters
force_download: false

# R specific
confidence_threshold: 0.01
use_normalized_intensities: FALSE
use_irt: TRUE
return_decoys: FALSE
remove_shared_spectronaut_proteingroups: FALSE
do_plot: TRUE
remove_lowconf: TRUE
one_psm_per_precursor: NA
collapse_peptide_by: sequence_modified
filter_min_detect: 3
filter_min_quant: 3
filter_fraction_detect: 0.75
filter_fraction_quant: 0.75
filter_by_contrast: TRUE
norm_algorithm_vsn: TRUE
norm_algorithm_vwmb: FALSE
norm_algorithm_modebetween_protein: TRUE
norm_algorithm_modebetween: FALSE
norm_algorithm_rlr: FALSE
norm_algorithm_msempire: FALSE
norm_algorithm_by_group: FALSE
norm_algorithm_all_group: TRUE
norm_algorithm_by_contrast: FALSE
rollup_algorithm: NA
dea_algorithm_deqms: TRUE
dea_algorithm_msempire: TRUE
dea_algorithm_msqrob: TRUE
dea_algorithm_ebayes: FALSE
dea_algorithm_msqrobsum: FALSE
dea_qval_signif: 0.05
dea_fc_signif: NA
dea_qvalue_threshold: 0.01
dea_log2foldchange_threshold: NA
output_qc_report: TRUE
output_abundance_tables: TRUE
output_dir: msdap_results
output_within_timestamped_subdirectory: TRUE