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config.yml
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config.yml
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# === Analysis configuration file ======================================================
# --- Configuration for `seqneut-pipeline` ---------------------------------------------
# for this test example the location is "../" but for real analyses it should almost
# certainly be "seqneut-pipeline'
seqneut-pipeline: ../
# for this test example the location is "../docs", but for real analyses it should
# almost certainly be "docs"
docs: ../docs
# change this to a good description of your project
description: |
# Test example for [seqneut-pipeline](https://github.com/jbloomlab/seqneut-pipeline)
This is a small toy-example created by subsetting a real experiment dataset.
See [https://github.com/jbloomlab/seqneut-pipeline](https://github.com/jbloomlab/seqneut-pipeline)
for the computer code and underlying numerical data.
See [here](https://github.com/jbloomlab/seqneut-pipeline/graphs/contributors) for a
list of all contributors to the pipeline.
viral_libraries:
pdmH1N1_lib2023_loes: data/viral_libraries/pdmH1N1_lib2023_loes.csv
H3N2_lib2023_Kikawa: data/viral_libraries/2023_H3N2_Kikawa.csv
viral_strain_plot_order: data/viral_strain_plot_order.csv
neut_standard_sets:
loes2023: data/neut_standard_sets/loes2023_neut_standards.csv
illumina_barcode_parser_params:
upstream: CTCCCTACAATGTCGGATTTGTATTTAATAG
downstream: ''
minq: 20
upstream_mismatch: 4
bc_orientation: R2
default_process_plate_qc_thresholds: &default_process_plate_qc_thresholds
avg_barcode_counts_per_well: 250 # 250 for this test, typically >= 500 for real experiments
min_neut_standard_frac_per_well: 0.005
no_serum_per_viral_barcode_filters:
min_frac: 0.0005
max_fold_change: 3
max_wells: 2
per_neut_standard_barcode_filters:
min_frac: 0.005
max_fold_change: 3
max_wells: 2
min_neut_standard_count_per_well: 500 # 500 for this test, typically >= 1000 for real experiments
min_no_serum_count_per_viral_barcode_well: 30
max_frac_infectivity_per_viral_barcode_well: 5
min_dilutions_per_barcode_serum_replicate: 6
default_process_plate_curvefit_params: &default_process_plate_curvefit_params
frac_infectivity_ceiling: 1
fixtop: [0.75, 1]
fixbottom: 0
fixslope: [0.8, 10]
default_process_plate_curvefit_qc: &default_process_plate_curvefit_qc
max_frac_infectivity_at_least: 0
goodness_of_fit: # EITHER R2 must be >= min_R2 or RMSD must be <= max_RMSD
min_R2: 0.7
max_RMSD: 0.1 # you may be able to increase this to more like 0.1
serum_replicates_ignore_curvefit_qc: []
barcode_serum_replicates_ignore_curvefit_qc: []
plates:
plate2:
group: serum
date: 2023-08-01
viral_library: pdmH1N1_lib2023_loes
neut_standard_set: loes2023
samples_csv: data/plates/plate2_samples.csv
manual_drops: {}
qc_thresholds:
<<: *default_process_plate_qc_thresholds
curvefit_params:
<<: *default_process_plate_curvefit_params
curvefit_qc:
<<: *default_process_plate_curvefit_qc
illumina_barcode_parser_params:
upstream2: GCTACA
upstream2_mismatch: 1
plate11:
group: serum
date: 2023-09-26
viral_library: pdmH1N1_lib2023_loes
neut_standard_set: loes2023
samples_csv: data/plates/plate11_samples.csv
manual_drops:
barcode_serum_replicates:
- [AGTCCTATCCTCAAAT, M099d0]
qc_thresholds:
<<: *default_process_plate_qc_thresholds
curvefit_params:
<<: *default_process_plate_curvefit_params
curvefit_qc:
<<: *default_process_plate_curvefit_qc
barcode_serum_replicates_ignore_curvefit_qc:
- [AGGTCAAGACCACAGG, M099d0]
illumina_barcode_parser_params:
upstream2: ATCGAT
upstream2_mismatch: 1
H3N2_plate:
group: pilot
date: 2024-03-04
viral_library: H3N2_lib2023_Kikawa
neut_standard_set: loes2023
samples_csv: data/plates/H3N2_samples.csv
manual_drops: {}
qc_thresholds:
<<: *default_process_plate_qc_thresholds
curvefit_params:
<<: *default_process_plate_curvefit_params
curvefit_qc:
<<: *default_process_plate_curvefit_qc
default_serum_titer_as: midpoint # can be "midpoint" or "nt50"
default_serum_qc_thresholds: &default_serum_qc_thresholds
min_replicates: 2
max_fold_change_from_median: 3
viruses_ignore_qc: []
sera_override_defaults:
serum:
M099d30:
qc_thresholds:
<<: *default_serum_qc_thresholds
viruses_ignore_qc:
- A/Belgium/H0017/2022
Y044d30:
qc_thresholds:
<<: *default_serum_qc_thresholds
max_fold_change_from_median: 4
titer_as: nt50
miscellaneous_plates:
random_plate_1:
date: 2023-08-01
viral_library: pdmH1N1_lib2023_loes
neut_standard_set: loes2023
samples_csv: data/miscellaneous_plates/random_plate_1.csv
illumina_barcode_parser_params:
upstream2: GCTACA
upstream2_mismatch: 1