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config_template.yaml
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config_template.yaml
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# Define paths to binaries and jar files
#philosopher_executable: "/cluster/projects/nn9864k/cmkobel/02_proteomics/bin/philosopher_v4.8.1_linux_amd64/philosopher"
#msfragger_jar: "/cluster/projects/nn9864k/cmkobel/02_proteomics/bin/MSFragger-3.7/MSFragger-3.7.jar"
#ionquant_jar: "/cluster/projects/nn9864k/cmkobel/02_proteomics/bin/IonQuant-1.8.10/IonQuant-1.8.10.jar"
#fragpipe_executable: "/cluster/projects/nn9864k/cmkobel/02_proteomics/bin/FragPipe-19.1/bin/fragpipe"
# Paths on glittertind
philosopher_executable: "/glittertind/shared_binaries/philosopher_v5.0.0/philosopher"
msfragger_jar: "/glittertind/shared_binaries/msfragger_v3.8/MSFragger-3.8/MSFragger-3.8.jar"
ionquant_jar: "/glittertind/shared_binaries/ionquant-v1.9.8/IonQuant-1.9.8/IonQuant-1.9.8.jar"
fragpipe_executable: "/glittertind/shared_binaries/fragpipe_v20.0/fragpipe/bin/fragpipe"
# Define parameters
# d_base points to the base of the d files.
# database_glob points to the database that the targets are made of. We can only search for proteins that we already know. I wonder if that is why we're doing transcriptomics, because we don't know how the DNA is redundantly translated?
# samples is a dictionary that points to all the samples within
batch_parameters: # Digesta at slaughter - Together with Puchun and Yanna
"220506_DnnT6_c6":
d_base: "/glittertind/projects/supacow/data/2022-05-06_PEP_timsTOF_D--T6S_24_andpuchun36/2022-05-06_PEP_timsTOF_D--T6S_24_andpuchun36/timsTOF/20220525_CMK"
database_glob: "/glittertind/projects/supacow/data/aa_databases/10_supacow/concatenate6/*.faa"
samples:
"D01T6S": "20220506_C9_Slot1-33_1_1971.d" # C 9
# # C10
"D02T6S": "20220506_C11_Slot1-35_1_1973.d" # C11
"D06T6S": "20220506_C12_Slot1-36_1_1974.d" # C12
#"unknown": "20220506_D1_Slot1-37_1_1975.d" # D 1
"D08T6S": "20220506_D2_Slot1-38_1_1976.d" # D 2
"D15T6S": "20220506_D3_Slot1-39_1_1977.d" # D 3
"D16T6S": "20220506_D4_Slot1-40_1_1978.d" # D 4
"D21T6S": "20220506_D5_Slot1-41_1_1979.d" # D 5
"D25T6S": "20220506_D6_Slot1-42_1_1980.d" # D 6
"D28T6S": "20220506_D7_Slot1-43_1_1981.d" # D 7
"D29T6S": "20220506_D8_Slot1-44_1_1982.d" # D 8
"D35T6S": "20220506_D9_Slot1-45_1_1983.d" # D 9
"D42T6S": "20220506_D10_Slot1-46_1_1984.d" # D10
"D43T6S": "20220506_D11_Slot1-47_1_1985.d" # D11
"D45T6S": "20220506_D12_Slot1-48_1_1986.d" # D12
"D48T6S": "20220506_E1_Slot1-49_1_1987.d" # E 1
"D51T6S": "20220506_E2_Slot1-50_1_1988.d" # E 2
"D55T6S": "20220506_E3_Slot1-51_1_1989.d" # E 3
"D59T6S": "20220506_E4_Slot1-52_1_1990.d" # E 4
"D60T6S": "20220506_E5_Slot1-53_1_1991.d" # E 5
"D61T6S": "20220506_E6_Slot1-54_1_1992.d" # E 6
"D63T6S": "20220506_E7_Slot1-55_1_1993.d" # E 7
"D67T6S": "20220506_E8_Slot1-56_1_1994.d" # E 8
"D75T6S": "20220506_E9_Slot1-57_1_1995.d" # E 9
"D76T6S": "20220506_E10_Slot1-58_1_1996.d" # E10
# Puchuns 32 digesta - Together with Puchun and Yanna - Swap project.
"220506_digesta_puchun":
d_base: "/glittertind/projects/supacow/data/2022-05-06_PEP_timsTOF_D--T6S_24_andpuchun36/2022-05-06_PEP_timsTOF_D--T6S_24_andpuchun36/timsTOF/20220525_CMK"
database_glob: "/glittertind/projects/supacow/data/aa_databases/10_supacow/c6_puchun/*.faa"
samples:
"P1": "20220506_A1_Slot1-01_1_1939.d" # A 1
"P2": "20220506_A2_Slot1-02_1_1940.d" # A 2
"P3": "20220506_A3_Slot1-03_1_1941.d" # A 3
"P4": "20220506_A4_Slot1-04_1_1942.d" # A 4
"P5": "20220506_A5_Slot1-05_1_1943.d" # A 5
"P6": "20220506_A6_Slot1-06_1_1944.d" # A 6
"P7": "20220506_A7_Slot1-07_1_1945.d" # A 7
"P8": "20220506_A8_Slot1-08_1_1946.d" # A 8
"P8v2": "20220506_A9_Slot1-09_1_1947.d" # A 9
"P9": "20220506_A10_Slot1-10_1_1948.d" # A10
"P10": "20220506_A11_Slot1-11_1_1949.d" # A11
"P11": "20220506_A12_Slot1-12_1_1950.d" # A12
"P12": "20220506_B1_Slot1-13_1_1951.d" # B 1
"P13": "20220506_B2_Slot1-14_1_1952.d" # B 2
"P14": "20220506_B3_Slot1-15_1_1953.d" # B 3
"P15": "20220506_B4_Slot1-16_1_1954.d" # B 4
"P16": "20220506_B5_Slot1-17_1_1955.d" # B 5
"P17": "20220506_B6_Slot1-18_1_1956.d" # B 6
"P18": "20220506_B7_Slot1-19_1_1957.d" # B 7
"P19": "20220506_B8_Slot1-20_1_1958.d" # B 8
"P20": "20220506_B9_Slot1-21_1_1959.d" # B 9
"P21": "20220506_B10_Slot1-22_1_1960.d" # B10
"P22": "20220506_B11_Slot1-23_1_1961.d" # B11
"P23": "20220506_B12_Slot1-24_1_1962.d" # B12
"P24": "20220506_C1_Slot1-25_1_1963.d" # C 1
"P25": "20220506_C2_Slot1-26_1_1964.d" # C 2
"P26": "20220506_C3_Slot1-27_1_1965.d" # C 3
"P27": "20220506_C4_Slot1-28_1_1966.d" # C 4
"P28": "20220506_C5_Slot1-29_1_1967.d" # C 5
"P29": "20220506_C6_Slot1-30_1_1968.d" # C 6
"P30": "20220506_C7_Slot1-31_1_1969.d" # C 7
"P31": "20220506_C8_Slot1-32_1_1970.d" # C 8
"P32": "20220506_C10_Slot1-34_1_1972.d" # C10
#"unknown": "20220506_D1_Slot1-37_1_1975.d" # D 1
"220926_WnnT6_c6": # Carl alone Wall
d_base: "/glittertind/projects/supacow/data/2022-09-26_PEP_timsTOF_LWD_Carl/20220901_Carl"
database_glob: "/glittertind/projects/supacow/data/aa_databases/10_supacow/concatenate6/*.faa"
samples:
"W25T6R": "20220921_A4_Slot1-04_1_2452.d" # A4
"W51T6R": "20220921_A5_Slot1-05_1_2453.d" # A5
"W76T6R": "20220921_A6_Slot1-06_1_2454.d" # A6
"W21T6R": "20220901_B4_Slot1-16_1_2458.d" # B4
"W48T6R": "20220901_B5_Slot1-17_1_2459.d" # B5
"W75T6R": "20220901_B6_Slot1-18_1_2460.d" # B6
"W16T6R": "20220901_C4_Slot1-28_1_2464.d" # C4
"W45T6R": "20220901_C5_Slot1-29_1_2465.d" # C5
"W67T6R": "20220901_C6_Slot1-30_1_2466.d" # C6
"W15T6R": "20220901_D4_Slot1-40_1_2475.d" # D4
"W43T6R": "20220901_D5_Slot1-41_1_2476.d" # D5
"W63T6R": "20220901_D6_Slot1-42_1_2477.d" # D6
"W08T6R": "20220901_E4_Slot1-52_1_2486.d" # E4
"W42T6R": "20220901_E5_Slot1-53_1_2487.d" # E5
"W61T6R": "20220901_E6_Slot1-54_1_2488.d" # E6
"W06T6R": "20220901_F4_Slot1-64_1_2497.d" # F4
"W35T6R": "20220901_F5_Slot1-65_1_2498.d" # F5
"W60T6R": "20220901_F6_Slot1-66_1_2499.d" # F6
"W02T6R": "20220901_G4_Slot1-76_1_2508.d" # G4
"W29T6R": "20220901_G5_Slot1-77_1_2509.d" # G5
"W59T6R": "20220901_G6_Slot1-78_1_2510.d" # G6
"W01T6R": "20220901_H4_Slot1-88_1_2519.d" # H4
"W28T6R": "20220901_H5_Slot1-89_1_2520.d" # H5
"W55T6R": "20220901_H6_Slot1-90_1_2521.d" # H6
"220926_LnnT6_dbB2": # Carl alone Liver
d_base: "/glittertind/projects/supacow/data/2022-09-26_PEP_timsTOF_LWD_Carl/20220901_Carl"
database_glob: "/glittertind/projects/supacow/data/aa_databases/10_supacow/concatenate6/dbB2.faa"
samples:
"L01T6R": "20220901_H1_Slot1-85_1_2516.d" # H1 H 1 L01
"L02T6R": "20220901_G1_Slot1-73_1_2505.d" # G1 G 1 L02
"L06T6R": "20220901_F1_Slot1-61_1_2494.d" # F1 F 1 L06
"L08T6R": "20220901_E1_Slot1-49_1_2483.d" # E1 E 1 L08
"L15T6R": "20220901_D1_Slot1-37_1_2472.d" # D1 D 1 L15
"L16T6R": "20220901_C1_Slot1-25_1_2461.d" # C1 C 1 L16
"L21T6R": "20220901_B1_Slot1-13_1_2455.d" # B1 B 1 L21
"L25T6R": "20220921_A1_Slot1-01_1_2449.d" # A1 A 1 L25
"L28T6R": "20220901_H2_Slot1-86_1_2517.d" # H2 H 2 L28
"L29T6R": "20220901_G2_Slot1-74_1_2506.d" # G2 G 2 L29
"L35T6R": "20220901_F2_Slot1-62_1_2495.d" # F2 F 2 L35
"L42T6R": "20220901_E2_Slot1-50_1_2484.d" # E2 E 2 L42
"L43T6R": "20220901_D2_Slot1-38_1_2473.d" # D2 D 2 L43
"L45T6R": "20220901_C2_Slot1-26_1_2462.d" # C2 C 2 L45
"L48T6R": "20220901_B2_Slot1-14_1_2456.d" # B2 B 2 L48
"L51T6R": "20220921_A2_Slot1-02_1_2450.d" # A2 A 2 L51
"L55T6R": "20220901_H3_Slot1-87_1_2518.d" # H3 H 3 L55
"L59T6R": "20220901_G3_Slot1-75_1_2507.d" # G3 G 3 L59
"L60T6R": "20220901_F3_Slot1-63_1_2496.d" # F3 F 3 L60
"L61T6R": "20220901_E3_Slot1-51_1_2485.d" # E3 E 3 L61
"L63T6R": "20220901_D3_Slot1-39_1_2474.d" # D3 D 3 L63
"L67T6R": "20220901_C3_Slot1-27_1_2463.d" # C3 C 3 L67
"L75T6R": "20220901_B3_Slot1-15_1_2457.d" # B3 B 3 L75
"L76T6R": "20220921_A3_Slot1-03_1_2451.d" # A3 A 3 L76
"220926_DnnTnS_c6": # Carl alone Digesta timeseries
d_base: "/glittertind/projects/supacow/data/2022-09-26_PEP_timsTOF_LWD_Carl/20220901_Carl"
database_glob: "/glittertind/projects/supacow/data/aa_databases/10_supacow/concatenate6/*.faa"
samples:
"D01T1S": "20220901_H7_Slot1-91_1_2522.d" # H7 H7 D01T1S
"D01T2S": "20220901_H8_Slot1-92_1_2523.d" # H8 H8 D01T2S
"D01T3S": "20220901_H9_Slot1-93_1_2524.d" # H9 H9 D01T3S
"D01T4S": "20220901_H10_Slot1-94_1_2525.d" # H10 H10 D01T4S
"D01T5S": "20220901_H11_Slot1-95_1_2526.d" # H11 H11 D01T5S
"D02T1S": "20220901_G7_Slot1-79_1_2511.d" # G7 G7 D02T1S
"D02T2S": "20220901_G8_Slot1-80_1_2512.d" # G8 G8 D02T2S
"D02T3S": "20220901_G9_Slot1-81_1_2513.d" # G9 G9 D02T3S
"D02T4S": "20220901_G10_Slot1-82_1_2514.d" # G10 G10 D02T4S
"D02T5S": "20220901_G11_Slot1-83_1_2515.d" # G11 G11 D02T5S
"D28T1S": "20220901_F7_Slot1-67_1_2500.d" # F7 F7 D28T1S
"D28T2S": "20220901_F8_Slot1-68_1_2501.d" # F8 F8 D28T2S
"D28T3S": "20220901_F9_Slot1-69_1_2502.d" # F9 F9 D28T3S
"D28T4S": "20220901_F10_Slot1-70_1_2503.d" # F10 F10 D28T4S
"D28T5S": "20220901_F11_Slot1-71_1_2504.d" # F11 F11 D28T5S
"D51T1S": "20220901_E7_Slot1-55_1_2489.d" # E7 E7 D51T1S
"D51T2S": "20220901_E8_Slot1-56_1_2490.d" # E8 E8 D51T2S
"D51T3S": "20220901_E9_Slot1-57_1_2491.d" # E9 E9 D51T3S
"D51T4S": "20220901_E10_Slot1-58_1_2492.d" # E10 E10 D51T4S
"D51T5S": "20220901_E11_Slot1-59_1_2493.d" # E11 E11 D51T5S
"D55T1S": "20220901_D7_Slot1-43_1_2478.d" # D7 D7 D55T1S
"D55T2S": "20220901_D8_Slot1-44_1_2479.d" # D8 D8 D55T2S
"D55T3S": "20220901_D9_Slot1-45_1_2480.d" # D9 D9 D55T3S
"D55T4S": "20220901_D10_Slot1-46_1_2481.d" # D10 D10 D55T4S
"D55T5S": "20220901_D11_Slot1-47_1_2482.d" # D11 D11 D55T5S
"D67T1S": "20220901_C7_Slot1-31_1_2467.d" # C7 C7 D67T1S
"D67T2S": "20220901_C8_Slot1-32_1_2468.d" # C8 C8 D67T2S
"D67T3S": "20220901_C9_Slot1-33_1_2469.d" # C9 C9 D67T3S
"D67T4S": "20220901_C10_Slot1-34_1_2470.d" # C10 C10 D67T4S
"D67T5S": "20220901_C11_Slot1-35_1_2471.d" # C11 C11 D67T5S
# copied from order.
batch: "220926_WnnT6_c6"
batch: "220926_LnnT6_dbB2"
batch: "220926_DnnTnS_c6"
batch: "220506_DnnT6_c6"
batch: "220506_digesta_puchun"