/*
 * -------------------------------------------------
 *  Nextflow config file for running full-size tests
 * -------------------------------------------------
 * Defines bundled input files and everything required
 * to run a full size pipeline test. Use as follows:
 *   nextflow run nf-core/diaproteomics -profile test_full,<docker/singularity>
 */

params {
  config_profile_name = 'Full test profile'
  config_profile_description = 'Full test dataset to check pipeline function'
  // Limit resources so that this can run on GitHub Actions
  max_cpus = 32
  max_memory = 16.GB
  max_time = 48.h
  pyprophet_classifier = 'LDA'  // LDA is conservative: Also possible to switch to XGBoost to do a non-linear target-decoy separation (risk overfitting)
  pyprophet_peakgroup_fdr = 0.01
  pyprophet_peptide_fdr = 0.01
  pyprophet_protein_fdr = 0.01
  pyprophet_global_fdr_level = 'protein'
  dialignr_global_align_fdr = 0.01
  dialignr_analyte_fdr = 0.01
  dialignr_unalign_fdr = 0.01
  dialignr_align_fdr = 0.05
  dialignr_query_fdr = 0.05
  min_overlap_for_merging = 10  // depending on the dataset it is possible to raise this value (minimum peptides that are shared for the RT alignment)
  irt_min_bins_covered = 8
  irt_alignment_method = 'lowess'
  n_irts = 250         // high number of pseudo irts for alignment between library and DIA run, if low yield samples are used this value can be smaller.
  generate_spectral_library = true   // specification that library should be generated from DDA input data
  generate_pseudo_irts = false        // specification that irt-library should be generated from DDA input data
  merge_libraries = true             // specification that multiple libraries belonging to the same sample group should be merged
  align_libraries = true             // specification that multiple libraries belonging to the same sample group should be RT aligned
  force_option = true                // specification that the OpenSwathWorkflow should be forced to run despite warnings
  generate_plots = true
  run_msstats = true

  // Input data
  input = 'https://raw.githubusercontent.com/nf-core/test-datasets/diaproteomics/sample_sheet_full.tsv'
  unimod = 'https://raw.githubusercontent.com/nf-core/test-datasets/diaproteomics/unimod.xml'
  input_sheet_dda = 'https://raw.githubusercontent.com/nf-core/test-datasets/diaproteomics/dda_sheet_full.tsv'
  irts = 'https://raw.githubusercontent.com/nf-core/test-datasets/diaproteomics/irt_sheet_full.tsv'
}
