Commit 0c638511 authored by Mathias Walzer's avatar Mathias Walzer
Browse files

added 1.4 config (switch background subtraction method and min peak width)

parent dc09e58d
sciex_converter:
container: "/hps/nobackup2/proteomics/sciex_converter_prideswath.simg"
memory: 4 # GB, multiplied by the number of attempts
maxRetries: 5
openswath:
container: "/hps/nobackup2/proteomics/openswath:0.1.2.simg"
memory: 4 # GB, multiplied by the number of attempts
threads: 6
mz_extraction_window: 30 # ppm
irt_mz_extraction_window: 50 #ppm
rt_extraction_window: 600 # seconds
background_subtraction: "original" # or none or exact
min_peak_width: 15 # default is -1 (i.e. no cut-off)
yamato:
container: "/hps/nobackup2/proteomics/yamato:v1.0.4_pridereswath.simg"
memory: 8 # GB, multiplied by the number of attempts
maxRetries: 3
pyprophet:
container: "/hps/nobackup2/proteomics/pyprophet_2.1.3.simg"
memory: 4 # GB, multiplied by the number of attempts
threads: 6
max_global_peptide_qvalue: 0.01
max_global_protein_qvalue: 0.01
max_rs_peakgroup_qvalue: 0.01
test: false
tric:
container: "/hps/nobackup2/proteomics/openswath:0.1.2.simg"
memory: 4 # GB, multiplied by the number of attempts
alignment_score: 0.0999
fdr_cutoff: 0.01
max_fdr_quality: 0.01
helper_scripts:
container: "/hps/nobackup2/proteomics/pridereswath.simg"
memory: 4
aRgh:
container: "/hps/nobackup2/proteomics/python-r:bioc-py3-tinytex-qc_plus_msstats.simg"
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