# Canonical control-probe IDs (spec QC-002). Keys are *normalised* names: case-folded, whitespace collapsed,
# no spaces next to or inside parentheses, "bgnd" written as "bkg". Several manifest spellings map to one ID.
canonical:
  # staining
  biotin(high): biotin_high
  biotin(bkg): biotin_bkg
  biotin(5k): biotin_5k
  dnp(high): dnp_high
  dnp(bkg): dnp_bkg
  dnp(20k): dnp_20k
  # extension
  extension(a): ext_A
  extension(t): ext_T
  extension(c): ext_C
  extension(g): ext_G
  # hybridization
  hyb(high): hyb_high
  hyb(medium): hyb_medium
  hyb(low): hyb_low
  # target removal
  target removal: target_removal_1
  target removal(1): target_removal_1
  target removal 1: target_removal_1
  target removal(2): target_removal_2
  target removal 2: target_removal_2
  # stringency
  string(pm): string_pm
  string(mm): string_mm
  # non-specific binding (one bead type per colour label on genotyping chips)
  nsb(bkg): nsb_bkg
  nsb(bkg) red: nsb_bkg
  nsb(bkg) green: nsb_bkg
  nsb(bkg) blue: nsb_bkg
  nsb(bkg) purple: nsb_bkg
  # non-polymorphic
  np(a): np_A
  np(t): np_T
  np(c): np_C
  np(g): np_G
  # restoration (FFPE)
  restoration: restoration
  restore: restoration
  # methylation (metrics in v2; names mapped already so controls_raw.tsv is labelled consistently)
  bs conversion i c1: bs1_C1
  bs conversion i c2: bs1_C2
  bs conversion i c3: bs1_C3
  bs conversion i c4: bs1_C4
  bs conversion i c5: bs1_C5
  bs conversion i u1: bs1_U1
  bs conversion i u2: bs1_U2
  bs conversion i u3: bs1_U3
  bs conversion i u4: bs1_U4
  bs conversion i u5: bs1_U5
  bs conversion i-c1: bs1_C1
  bs conversion i-c2: bs1_C2
  bs conversion i-c3: bs1_C3
  bs conversion i-c4: bs1_C4
  bs conversion i-c5: bs1_C5
  bs conversion i-c6: bs1_C6
  bs conversion i-u1: bs1_U1
  bs conversion i-u2: bs1_U2
  bs conversion i-u3: bs1_U3
  bs conversion i-u4: bs1_U4
  bs conversion i-u5: bs1_U5
  bs conversion i-u6: bs1_U6
  bs conversion i c6: bs1_C6
  bs conversion i u6: bs1_U6
  bs conversion ii-1: bs2_1
  bs conversion ii-2: bs2_2
  bs conversion ii-3: bs2_3
  bs conversion ii-4: bs2_4
  gt mismatch 1(pm): gtmm_1_pm
  gt mismatch 2(pm): gtmm_2_pm
  gt mismatch 3(pm): gtmm_3_pm
  gt mismatch 4(pm): gtmm_4_pm
  gt mismatch 5(pm): gtmm_5_pm
  gt mismatch 6(pm): gtmm_6_pm
  gt mismatch 1(mm): gtmm_1_mm
  gt mismatch 2(mm): gtmm_2_mm
  gt mismatch 3(mm): gtmm_3_mm
  gt mismatch 4(mm): gtmm_4_mm
  gt mismatch 5(mm): gtmm_5_mm
  gt mismatch 6(mm): gtmm_6_mm
  specificity 1: spec2_1
  specificity 2: spec2_2
  specificity 3: spec2_3

# Categories treated as methylation-only (dataset type detection, QC-043).
methylation_categories:
  - bisulfite conversion i
  - bisulfite conversion ii
  - specificity i
  - specificity ii

# Report exclusion list (QC-010): raw-probe views leave these out; derived metrics still use them.
report_exclude:
  categories: [negative, norm]
  names: ["np(g) 1", "np(g) 2", "np(g) 3", "np(g) 4", "np(g) 5", "biotin(5k)", "dnp(20k)"]