config.yml

test_files:
  # Cytoflex
  - src:
      zip_url: https://zenodo.org/records/15019428/files/Fig3A_human%20organoids_Raw%20data.zip
      dataset_id: zenodo_CytoFlex
      file_paths:
        - Fig3A_human organoids_Raw data/D110_stained.fcs
        - Fig3A_human organoids_Raw data/D110_unstained.fcs
        - Fig3A_human organoids_Raw data/D110_unstained_new.fcs

  # Apogee A60 Micro
  - src:
      zip_url: https://zenodo.org/records/4561815/files/Figure_2.zip
      dataset_id: zenodo_ApogeeA60micro
      file_paths:
        - Figure_2/2b/02_Si_182nm_dil1E5.fcs
        - Figure_2/2b/04_Si_315nm_dil1E5.fcs
        - Figure_2/2b/05_Si_321nm_dil1E5.fcs
        - Figure_2/2b/06_Si_405nm_dil1E4.fcs
        - Figure_2/2b/07_Si_548nm_dil1E4.fcs
    parse:
      machine: apo_a60micro
      strategy: scalpal

  # easycyte
  - src:
      zip_url: https://zenodo.org/records/10720746/files/Co-cultures_data.zip
      dataset_id: zenodo_easycyte
      file_paths:
        - Direct co-cultures/EXP007_2022-01-19_at_04-01-12pm.fcs
        - Direct co-cultures/EXP007_2022-01-20_at_02-07-37pm.fcs
        - Direct co-cultures/EXP007_2022-01-21_at_02-31-36pm.fcs
    parse:
      machine: cytek_easycyte

  # Aurora
  - src:
      url_root: https://zenodo.org/records/15723074/files/B_cells_donor1.fcs
      dataset_id: zenodo_Aurora
      filemap:
        b_d1.fcs: B_cells_donor1.fcs
        b_d2.fcs: B_cells_donor2.fcs
        b_d3.fcs: B_cells_donor3.fcs
        t4_d1.fcs: Effector_memory_CD4+_T%20cells_donor1.fcs
        t4_d2.fcs: Effector_memory_CD4+_T%20cells_donor2.fcs
        t4_d3.fcs: Effector_memory_CD4+_T%20cells_donor3.fcs
        t8_d1.fcs: Effector_memory_CD8+_T_cells_donor1.fcs
        t8_d2.fcs: Effector_memory_CD8+_T_cells_donor2.fcs
        t8_d3.fcs: Effector_memory_CD8+_T_cells_donor3.fcs

  # Sony SA3800
  - src:
      url_root: https://zenodo.org/records/7971252/files/
      dataset_id: zenodo_SonySA3800
      filemap:
        a1.fcs: A01%20Well%20-%20A01%20WLSM.fcs
        a2.fcs: A02%20Well%20-%20A02%20WLSM.fcs
        a3.fcs: A03%20Well%20-%20A03%20WLSM.fcs

  # Attune NxT
  - src:
      url_root: https://zenodo.org/records/7352402/files/
      dataset_id: zenodo_AttuneNxt
      filemap:
        bl1.fcs: Tmem119%20x%20IAB%20AAV%20NJG%201.6.22_Compensation_BL1-A.fcs
        bl3.fcs: Tmem119%20x%20IAB%20AAV%20NJG%201.6.22_Compensation_BL3-A.fcs
        rl1.fcs: Tmem119%20x%20IAB%20AAV%20NJG%201.6.22_Compensation_RL1-A.fcs
        rl3.fcs: Tmem119%20x%20IAB%20AAV%20NJG%201.6.22_Compensation_RL3-A.fcs
    parse:
      machine: thermo_attune_nxt

  # Helios (according to https://elifesciences.org/reviewed-preprints/95494v2)
  - src:
      url_root: https://zenodo.org/records/7982165/files/
      dataset_id: zenodo_Helios
      filemap:
        am_non_jak2.fcs: AM_Non_JAK2.fcs
        cj_jakj2.fcs: CJ_JAK2.fcs
        fd_non_jak2.fcs: FD_Non_JAK2.fcs
    parse:
      machine: sbt_helios
        
  # FACSDiscover A8
  - src:
      url_root: https://zenodo.org/records/15726118/files/
      dataset_id: zenodo_FACSDiscoverA8
      filemap:
        hd20_bm.fcs: HD%20BM%201.fcs
        hd_pbmc.fcs: HD%20PBMC.fcs
    parse:
      options:
        allow_other_feature: true

  # Imagestream
  - src:
      url_root: https://zenodo.org/records/15726118/files/
      dataset_id: zenodo_Imagestream
      filemap:
        no_ab.fcs: No%20ab%202_3.fcs
        ritux.fcs: Ritux%202_5.fcs

  # FASCLyric
  - src:
      url_root: https://zenodo.org/records/17222100/files/
      dataset_id: zenodo_FACSLyric
      filemap:
        4g2_t1.fcs: 20250409_DV2_4G2_T1_340.fcs
        4g2_t2.fcs: 20250409_DV2_4G2_T2_340_001.fcs
        4g2_t3.fcs: 20250409_DV2_4G2_T3_340.fcs
        scfv_t1.fcs: 20250409_DV2_SCFV_T1_400.fcs
        scfv_t2.fcs: 20250409_DV2_SCFV_T2_400.fcs
        scfv_t3.fcs: 20250409_DV2_SCFV_T3_400.fcs

  # FASCSymphony A5
  - src:
      url_root: https://zenodo.org/records/13928969/files/
      dataset_id: zenodo_FACSSymphonyA5
      filemap:
        p1_tp1.fcs: ID1_Panel1_TP1.fcs
        p1_tp2.fcs: ID1_Panel1_TP2.fcs
        p1_tp3.fcs: ID1_Panel1_TP3.fcs
        # $CYT for this file says its from a Fortessa (shrug emoji)
        # p2_tp1.fcs: ID1_Panel2_TP1.fcs
        p2_tp2.fcs: ID1_Panel2_TP2.fcs
        p2_tp3.fcs: ID1_Panel2_TP3.fcs
    parse:
      machine: bd_symph_a5
  
  # FACSCalibur (https://www.sciencedirect.com/science/article/pii/S0091674907010299?via%3Dihub)
  - src:
      immport_id: SDY1
      file_names:
        - 02054141.003.52632.fcs
    parse:
      options:
        time_meas_pattern: null

  # FACSCalibur
  - src:
      immport_id: SDY194
      file_names:
        - 100.204.414416.fcs
        - 100R.205.414418.fcs
    parse:
      options:
        time_meas_pattern: null

  # FACSCalibur
  - src:
      immport_id: SDY199
      file_names:
        - SUB120119_0041C0404A001_002.346966.fcs
        - SUB120119_0041C0404A001_003.346968.fcs
        - SUB120119_0041C0404A001_004.346970.fcs
    parse:
      options:
        time_meas_pattern: null

  # FACSCalibur
  - src:
      immport_id: SDY217
      file_names:
        - Data.001 day 10 ova alone.393110.fcs
        - Data.001 day 4 ova alone.393102.fcs
        - Data.001 day 5 no antigen.393086.fcs
    parse:
      options:
        time_meas_pattern: null

  # machine not mentioned in $CYT, pub says it was a FACScan (see https://pmc.ncbi.nlm.nih.gov/articles/PMC3082611)
  - src:
      immport_id: SDY4
      file_names:
        - ES481973.248766.fcs
        - ES481974.248771.fcs
        - ES481975.248774.fcs
    parse:
      machine: bd_facscan

  # LSRII (according to https://pmc.ncbi.nlm.nih.gov/articles/PMC3585146/ and
  # https://pmc.ncbi.nlm.nih.gov/articles/PMC3469550/)
  - src:
      immport_id: SDY100
      file_names:
        - 138085.294085.fcs
        - 138086.294088.fcs
        - 138087.294090.fcs
    parse:
      machine: bd_lsr2

  # LSRII according to https://pmc.ncbi.nlm.nih.gov/articles/PMC5728448/#sec4
  - src:
      immport_id: SDY1176
      file_names:
        - 082.661592.fcs
        - 083.661593.fcs
        - 084.661594.fcs
        - 1292966.652906.fcs
        - 1292968.652920.fcs
        - 1292970.652921.fcs
    parse:
      machine: bd_lsr2

  # LSRII according to https://pmc.ncbi.nlm.nih.gov/articles/PMC6559862/#Sec10
  - src:
      immport_id: SDY1385
      file_names:
        - Compensation_AViD AmCyan_194.721484.fcs
        - Compensation_AViD AmCyan_202.721723.fcs
        - Compensation_AViD AmCyan_222.722173.fcs
        - Specimen_001_A10_A10_010.722002.fcs
        - Specimen_001_A10_A10_010.722262.fcs
        - Specimen_001_A10_A10_050.722037.fcs
    parse:
      machine: bd_lsr2

  # LSRII
  # TODO find pub to confirm
  - src:
      immport_id: SDY9
      file_names:
        - Compensation Controls_7AAD PE-Cy5 Stained Control.240026.fcs
        - Compensation Controls_7AAD Stained Control--0010.239801.fcs
        - Compensation Controls_7AAD Stained Control--0011.239826.fcs

  # LSRII (based on $CYT, pub here does not mention machine: https://pmc.ncbi.nlm.nih.gov/articles/PMC3723701/#S2)
  - src:
      immport_id: SDY28
      file_names:
        - rk012909__001.174865.fcs
        - rk012909__002.174868.fcs
        - rk012909__003.174870.fcs
    parse:
      options:
        time_meas_pattern: null

  # LSRII
  - src:
      immport_id: SDY1015
      file_names:
        - E04_AI_T01_Compensation Controls_B 530,2f,30 Stained Control.615893.fcs
        - E04_AI_T01_Compensation Controls_B 710,2f,50 Stained Control.615894.fcs
        - E04_AI_T01_Compensation Controls_R 670,2f,30 Stained Control.615895.fcs
        - E04D01IIMMCYXXPL_090613RFa14PANELZ_1980215.616295.fcs
        - E04D01IIMMCYXXPL_090613RFv13PANELZ_1980216.616299.fcs
        - E04D01IIMMCYXXPL_090613RIc14PANELZ_1980219.616300.fcs

  # LSRII
  - src:
      immport_id: SDY1041
      file_names:
        - Compensation TF 07242015_PerCP-Cy5-5 Stained Control.625600.fcs
        - Compensation TF 07242015_PE-Texas Red Stained Control.625598.fcs
        - Compensation TF 07242015_QDot 705 Stained Control.625608.fcs
        - D146 Ex A2 NLV_Bld.624444.fcs
        - D146 Ex A2 NLV_BM.624461.fcs
        - D146 Ex A2 NLV_Col.624465.fcs

  # LSRII
  - src:
      immport_id: SDY1086
      file_names:
        - 06092015-VAX002-TFH-Day0_ABX10.720881.fcs
        - 06092015-VAX002-TFH-Day0_ABX14.720888.fcs
        - 06092015-VAX002-TFH-Day0_ABX15.720890.fcs
        - 06092015-VAX002-TFH-Day7_Tfh-Control.720880.fcs
        - 0614PB_ABX-CTRL.721004.fcs
        - 0614Tfh_ABX-Control.720930.fcs

  # LSRII
  - src:
      immport_id: SDY1302
      file_names:
        - NGL010_Compensation Controls_Blue A 710,2f,50 Stained Control.700173.fcs
        - NGL010_Compensation Controls_Blue B 515,2f,20 Stained Control.700174.fcs
        - NGL010_Compensation Controls_Green A 780,2f,40 Stained Control.700175.fcs
        - PROP0510192-1_NOAG_A01.697887.fcs
        - PROP0510192-1_SEB_D01.697888.fcs
        - PROP0510192-1_TPHE_A01.700465.fcs
    parse:
      machine: bd_lsr2

  # FACSCantoII

  # TODO not sure what machine this actually is, this pub
  # (https://pmc.ncbi.nlm.nih.gov/articles/PMC3023136/) says either
  # FACSVantage or AriaII, and this pub (a protocol,
  # https://pmc.ncbi.nlm.nih.gov/articles/PMC2750034/) says FACS Aria, neither
  # of which are CantoII
  - src:
      immport_id: SDY33
      file_names:
        - ES128227.109527.fcs
        - ES128228.112011.fcs
        - ES128229.111526.fcs

  # CyTOF (5.1.562)
  # according to https://pmc.ncbi.nlm.nih.gov/articles/PMC6686855/#S10 this
  # was a cytof1 since these were acquired 2010-2013
  - src:
      immport_id: SDY112 
      file_names:
        - 081712-Mike-Study 15-2011-15026_cells_found.504108.fcs
        - 081712-Mike-Study 15-2011-15028_cells_found.504109.fcs
        - 081712-Mike-Study 15-2011-15029_cells_found.504110.fcs
    parse:
      machine: sbt_cytof

  # FACScan
  # TODO could not find machine in pub
  - src:
      immport_id: SDY196
      file_names:
        - SUB120116_004C0104A001_001.346425.fcs
        - SUB120116_004C0104A001_002.346428.fcs
        - SUB120116_004C0104A001_003.346430.fcs
        - SUB120116_004C0104A001_004.346432.fcs
        - SUB120116_004C0104A001_006.346436.fcs
        - SUB120116_004C0104A001_008.346440.fcs
    parse:
      options:
        time_meas_pattern: null

  # FACScan
  - src:
      immport_id: SDY241
      file_names:
        - 10374c.137534.fcs
        - 10374l.137586.fcs
        - 10374m.137530.fcs
    parse:
      options:
        time_meas_pattern: null

  # FACSCanto
  - src:
      immport_id: SDY284
      file_names:
        - 082808amhC1_Tube_001.177408.fcs
        - 082808amhC1_Tube_002.177410.fcs
        - 082808amhC1_Tube_003.177412.fcs

  # FACSAria
  - src:
      immport_id: SDY506
      file_names:
        - Compensation Specimen_APC CD8 Stained Control.515710.fcs
        - Compensation Specimen_FITC- CD107AB Stained Control.515711.fcs
        - Compensation Specimen_PE DextramerStained Control.515712.fcs

  # FACSAriaII
  - src:
      immport_id: SDY820
      file_names: 
        - Specimen_001_TP0001_001.605667.fcs
        - Specimen_001_TP0003_002.605679.fcs
        - Specimen_001_TP0004_001.605680.fcs

  # FACSAriaIII
  - src:
      immport_id: SDY997
      file_names:
        - 090616_200-0104-K_001.627795.fcs
        - 090616_200-0127-K_002.627836.fcs
        - 090616_200-0608-K_003.627877.fcs
        
  # cytof2 according to https://pmc.ncbi.nlm.nih.gov/articles/PMC5499363/#sec8
  - src:
      immport_id: SDY1100
      file_names: 
        - 151110_ASE001_758_moDC_DV2_8h.626416.fcs
        - 151110_ASE001_758_moDC_DV4_8h.626420.fcs
        - 151110_ASE001_758_moDC_mock_8h.626412.fcs
    parse:
      machine: sbt_cytof2
      options:
        dataset_overflow_limit: 12

  # cytof2 according to https://pmc.ncbi.nlm.nih.gov/articles/PMC5312823/
  - src:
      immport_id: SDY1108
      file_names:
        - TIN_BLD1_B6Antibodies_Day3.627157.fcs
        - TIN_BLD1_B6Antibodies_Day8.627160.fcs
        - TIN_BLD1_CD1Antibodies_Day3.627162.fcs
    parse:
      machine: sbt_cytof2

  # Fortessa
  - src:
      immport_id: SDY1115
      file_names:
        - Adult001_comp_24hrs_Compensation Controls_405B Stained Control_005.632043.635139.fcs

  - src:
      immport_id: SDY1115
      file_names:
        - Adult001_comp_24hrs_Compensation Controls_405 D 525,2f,50 Stained Control_004.632124.635137.fcs
        - Adult001_comp_24hrs_Compensation Controls_405 E 450,2f,50 Stained Control_003.632069.635138.fcs

  - src:
      immport_id: SDY1115
      file_names:
        - Adult001_HRV_24hrs.632136.635136.fcs
        - Adult001_unstim_24hrs.632137.635146.fcs

  # TODO this is one of the CyTOF instruments but there is no pub, we might be
  # able to assume this was a sbt_cytof1 based on the software version 1.0
  - src:
      immport_id: SDY1396
      file_names:
        - Sample_172169_Day1_WBC_15July2020_01_1.808052.fcs
        - Sample_172169_Month3_WBC_15July2020_01_1.808053.fcs
        
  # NovoCyte
  - src:
      immport_id: SDY1502
      file_names:
        - Specimen1_1-1.732826.fcs
        - Specimen1_1-1.732945.fcs
        - Specimen1_1-10.732949.fcs
    parse:
      options:
        nonstandard_measurement_pattern: "#NCP%n"

  # Aurora
  - src:
      immport_id: SDY1625
      file_names:
        - 1115 - DE 11 color panel.794843.fcs
        - 1115 - DE 4 color.744375.fcs
        - 1160 - DE 11 color panel.794855.fcs
        - 1689 - DE Isotypes.744381.fcs
        - 1689 - FM-AF488.744376.fcs
        - 1689 - FM-APC.744377.fcs

  # Attune
  - src:
      immport_id: SDY1655
      file_names:
        - 2020-03-18_HuMyl_Drop001_Experiment_Group_D3.774192.fcs
        - 2020-03-18_HuMyl_Drop001_Experiment_Group_D5.774194.fcs
        - 2020-03-18_HuMyl_Drop001_Experiment_Group_D7.774195.fcs
    parse:
      machine: thermo_attune_nxt


  # FACSverse
  - src:
      immport_id: SDY1666
      file_names:
        - 12-219-1.784751.fcs
        - 12-219-2.784753.fcs
        - 12-Mock-1.784754.fcs

  # helios according to https://www.science.org/doi/10.1126/science.abc6261#supplementary-materials
  # and file:///home/ndwar/Downloads/abc6261_arunachalam_sm.pdf
  - src:
      immport_id: SDY1669
      file_names:
        - c01_Batch2_1_singles_P11.858221.fcs
        - c01_Batch3_1_singles_P09.858243.fcs
        - c01_Batch4_1_singles_P10.858266.fcs
    parse:
      machine: sbt_helios

  # Cytek DxP10 (actually a FACScan)
  - src:
      immport_id: SDY1944
      file_names:
        - direct_kit_baso_300uL_1_VD5_20211019.853079.fcs
        - direct_kit_baso_300uL_2_VD5_20211019.853081.fcs
        - direct_kit_baso_300uL_3_VD1_20211007.853082.fcs
        - WBC_100uL_control_VD1_07312021.853011.fcs
        - WBC_100uL_control_VD1_20210803.853016.fcs
        - WBC_100uL_control_VD1_20210812.853019.fcs

  # cytof2
  - src:
      immport_id: SDY2947
      file_names:
        - CCR4-FMO.1208727.fcs
        - CCR6-FMO.1208728.fcs
        - CCR7-FMO.1208729.fcs
    parse:
      options:
        time_meas_pattern: null

  # ZE5
  - src:
      immport_id: SDY1640
      # TODO these first three need an additional correction for DATA in HEADER,
      # but this won't work now in the larger group because the correction is
      # also blindly applied to empty offsets, so 0,0 -> 0,-1
      file_names:
        # - A10 IL-10-APC.771563.fcs
        # - A1 CD4-BV605.771554.fcs
        # - A1 CXCR3-BV421.787857.fcs
        - A1 1592-AK-2  DMSO.771568.fcs
        - A1 1592-AK-2  DMSO.787875.fcs
        - A1 2109-AK-1  DMSO.787905.fcs

  # FACSCelesta
  - src:
      immport_id: SDY2583
      file_names:
        - DBG100_CP10.1137063.fcs
        - DBG100_CP16.1137913.fcs
        - DBG100_CP22.1138763.fcs

  # Fortessa X-20
  - src:
      immport_id: SDY1734
      file_names:
        - Alexa_Fluor_488_C_053.807010.fcs
        - Alexa_Fluor_647_C_055.807011.fcs
        - APC-Cy7_C_057.807014.fcs

  # Fortessa X-20
  - src:
      immport_id: SDY1734
      file_names:
        - L1-001_C-1_PfRBC.807009.fcs
        - L1-001_C-1_uRBC.807097.fcs
        - L1-001_D11_PfRBC.807025.fcs
    parse:
      options:
        time_meas_pattern: null

  # easycyte (according to https://pmc.ncbi.nlm.nih.gov/articles/PMC8026190/#sec11)
  - src:
      immport_id: SDY1680
      file_names:
        - 07B_G10_G10_082.786252.fcs
        - 07B_G12_G12_084.786253.fcs
        - 07B_G2_G02_074.786248.fcs
        - Comps2_A8_A08_068.786629.fcs
        - Comps2_A8_A08_070.786608.fcs
        - Comps2_B8_B08_070.786630.fcs
    parse:
      machine: cytek_easycyte

  # Helios (according to https://pmc.ncbi.nlm.nih.gov/articles/PMC8761119/#S10)
  - src:
      immport_id: SDY2189
      file_names:
        - c01_B1_singlets_null_Singlets_2047_12_24_20.1031667.fcs
        - c01_B2_singlets_null_Singlets_2050_12_24_20.1031686.fcs
        - c01_B3_singlets_null_Singlets_2049_12_24_20.1031680.fcs
    parse:
      machine: sbt_helios

  # Each of these Accuri files has roughly the same set of problems
  # - DATA offset end is 1 too high
  # - STEXT doesn't exist but overlaps with TEXT (and is weirdly very different)
  # - in some case DATA in TEXT is wildly off (its safe to ignore since HEADER
  #   is correct)
  - src:
      fr_id: FR-FCM-ZZZ4
      file_names:
        - Accuri - C6.fcs
    # parse:
    #   options:
    #     # I'm assuming these are centiseconds and not 1/60th seconds since they
    #     # exceed 59 but never exceed 99
    #     time_pattern: "%H:%M:%S:%@"
  
  - src:
      fr_id: FR-FCM-ZZZ4
      file_names:
        - Accuri - C6 - A01 H2O.fcs
        - Accuri - C6 - A02 Spherotech 8 Peak Beads.fcs
        - Accuri - C6 - A03 HPB - CD45 PerCP.fcs
    parse:
      options:
        # supp text partially overlaps (not clear why)
        ignore_supp_text: true
        # time_pattern: "%H:%M:%S:%@"
  
  - src:
      fr_id: FR-FCM-ZZZ4
      file_names:
        - 1 WT_001.fcs
        - BD - FACS Aria II - Compensation Controls_B515 Stained Control.fcs
        - BD - FACS Aria II - Compensation Controls_G560 Stained Control.fcs
        - BD - FACS Aria II - Compensation Controls_G610 Stained Control.fcs
        - BD - FACS Aria II - Compensation Controls_G660 Stained Control.fcs
        - Beckman Coulter - MoFlo Astrios - linear settings.fcs
        - Beckman Coulter - MoFlo Astrios - log settings.fcs
        - Beckman Coulter - MoFlo XDP.fcs
        - Cytek DxP10 - 6-peak Q&b 11-06-2012 001.fcs
        - Cytek DxP10 - APC COMP BEADS011.fcs
        - Cytek DxP10 - BLANK COMP BEADS007.fcs
        - Cytek DxP10 - FITC COMP BEADS008.fcs
        - Cytek DxP10 - PERCP COMP BEADS010.fcs
        - Cytek DxP10 - PE COMP BEADS009.fcs
        - iCyt - Eclipse.lmd
        - iCyt - Eclipse - 8 peak.lmd
        - iCyt - Eclipse - 20100922_14h35m49s(Protocol CytoTrol, Well C7).lmd
        - iCyt - Eclipse - 20100923_12h23m41s(Protocol Cell Cycle DAPI , SampleID1 DAPI Prep-DNA, Well A1).lmd
        - iCyt - Eclipse - 20100924_08h32m40s(Protocol AlignCheck - Final Test 6Runs, Well A1).lmd


  # actually a FACScan with a Cytek xP5 upgrade, "FACScan" is in the "nickname" field
  - src:
      fr_id: FR-FCM-ZZZ4
      file_names:
        - 3215apc 100004.fcs
    parse:
      machine: bd_facscan

  - src:
      fr_id: FR-FCM-ZZZ4
      file_names:
        - Applied Biosystems - Attune.fcs
    parse:
      machine: thermo_attune

  - src:
      fr_id: FR-FCM-ZZZ4
      file_names:
        - BD - FACS Aria II.fcs
    
  - src:
      fr_id: FR-FCM-ZZZ4
      file_names:
        - BD - FACS Aria II - Compensation Controls_G710 Stained Control.fcs
    parse:
      options:
        # this file appears to be cut in half
        data_correction: [0, -189504]
        replace_standard_key_values: {TOT: "6052"}
  
  - src:
      fr_id: FR-FCM-ZZZ4
      file_names:
        - Beckman Coulter - Cyan.fcs
    parse:
      machine: bc_cyan
      options:
        # one of the OTHER segments drove off the cliff at the end of the file
        max_other: 0
  
  - src:
      fr_id: FR-FCM-ZZZ4
      file_names:
        - Beckman Coulter - Cytomics FC500.LMD
    parse:
      options:
        time_meas_pattern: null
  
  - src:
      fr_id: FR-FCM-ZZZ4
      file_names:
        - Beckman Coulter - Gallios.LMD
        
  - src:
      fr_id: FR-FCM-ZZZ4
      file_names:
        - MVa2011-06-30_fcs30.fcs
        - MVa2011-06-30_fcs30c.fcs
    parse:
      machine: miltenyi_mqa
      options:
        time_meas_pattern: HDR-T


  - src:
      fr_id: FR-FCM-ZZZ4
      file_names:
        - MVa2011-06-30_fcs31.fcs
    parse:
      machine: miltenyi_mqa
      
  - src:
      fr_id: FR-FCM-ZZZ4
      file_names:
        - Miltenyi Biotec - MACSQuant Analyzer.fcs
    parse:
      machine: miltenyi_mqa
      options:
        time_meas_pattern: "HDR-TM"

  - src:
      fr_id: FR-FCM-ZZZ4
      file_names:
        - Millipore - easyCyte 6HT-2L - InCyte.fcs
    parse:
      machine: cytek_easycyte
  
  - src:
      fr_id: FR-FCM-ZZZ4
      file_names:
        - Partec - PAS - 8 peak beads.FCS
  
  - src:
      fr_id: FR-FCM-ZZZ4
      file_names:
        - Stratedigm - S1400 - 8 Peaks Beads.fcs
    parse:
      machine: strat_s1400
      
  - src:
      fr_id: FR-FCM-ZZZ4
      file_names:
        - System II listmode with extra info in bits D10-D15.LMD
    parse:
      machine: bc_system2
      options:
        time_meas_pattern: null
        
  - src:
      fr_id: FR-FCM-ZZZ4
      file_names:
        - Verity Software House - GemStoneGeneratedData - 500000events.fcs
    parse:
      machine: verity_gemstone
      options:
        # warnings_are_errors: false
        time_meas_pattern: null
  
  - src:
      fr_id: FR-FCM-ZZM3
      file_names:
        - 1c B_ALL_FCV DNA  LOW EVENTS .LMD 
        - 2c B_ALL_FCV DNA  LOW EVENTS.LMD
        - 3c B_ALL_FCV DNA  LOW EVENTS.LMD
        - 4c B_ALL_FCV DNA  LOW EVENTS.LMD
        - 5c B_ALL_FCV DNA  LOW EVENTS.LMD
        - 6c B_ALL_FCV DNA  LOW EVENTS.LMD
        - 7c B_ALL_FCV DNA  LOW EVENTS.LMD

  # Sony ID7000
  - src:
      fr_id: FR-FCM-Z7CH
      file_names:
        - B02 Unstained WLSM.fcs
        - B03 BUV395 WLSM.fcs
        - B04 BUV496 WLSM.fcs

  # FACSDiscover S8
  - src:
      fr_id: FR-FCM-Z73V
      file_names:
        - Unstained Monocytes_001.fcs
    parse:
      options:
        allow_other_feature: true
        # trim_value_whitespace: trim_blank_silent

  # Partec PAS
  - src:
      fr_id: FR-FCM-Z45W
      file_names:
        - Solanum_pseudocapsicum_fruit-skin.FCS
        - Solanum_pseudocapsicum_mature-leaf.FCS
        - Solanum_pseudocapsicum_petal-blades.FCS
        - Solanum_pseudocapsicum_root.FCS
        - Solanum_pseudocapsicum_stem.FCS
        - Solanum_pseudocapsicum_young-leaf.FCS

  # MoFlo XDP (with mixed byteord)
  - src:
      fr_id: FR-FCM-ZZY9
      file_names:
        - 29C6hr_1.fcs
        - 29C6hr_2.fcs
        - 29C6hr_3.fcs