Spectronaut-nf/params.yaml at main · BenCollinsLab/Spectronaut-nf · GitHub

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## Required

JOB_NAME: "251020_THP1_DMSO_Search_SN20.2"
spec_bin: "/users/3054755/bin/spectronaut/Spectronaut_20.2.250922.92449/binaries/Spectronaut/bin/SpectronautCMD.dll"
license: "/users/3054755/license/spec_license_no_var.txt"
#rawfile_dir: "/mnt/scratch2/users/3058937/MZ1_THP1/RAWFILES/"
FASTA: "uniprotkbHUMAN20240104.bgsfasta"

## Optional (can be left out, defaults kick in)
# sample_size: 104
batch_size: 2 # If not used, the is default is searching individual raw file for library (Pulsar)
excludePattern: "pooled"

COND_SETUP: "ConditionSetup.tsv"
REPORT: "Precursor_fragment_info.rs"
# PROP_DIA: "Kuiper_PTM_Probing_Search.prop"
EXT_PSAR: "251020_THP1_DMSO_Search_SN20.2.psar"

### Number of Parallel Searches ###
executor_queueSize: 4

### Process-specific Resource Allocation ####

# Random Sampling
# random_sampling_cpus: 4
# random_sampling_memory: '4 GB'
# random_sampling_time: '03:00:00'

#Pulsar search
SN_nf_pulsar_queue: 'k2-medpri,k2-fmipr'
SN_nf_pulsar_cpus: 64
SN_nf_pulsar_memory: '128 GB'
SN_nf_pulsar_time: '3:00:00'

#Library generation from combining multiple PSAR
SN_nf_combine_psar_queue: 'k2-medpri,k2-fmipr'
SN_nf_combine_psar_cpus: 64
SN_nf_combine_psar_memory: '128 GB'
SN_nf_combine_psar_time: '3:00:00'

#Raw file/Batch-specific DIA search
SN_nf_dia_search_queue: 'k2-medpri,k2-fmipr'
SN_nf_dia_search_cpus: 64
SN_nf_dia_search_memory: '128 GB'
SN_nf_dia_search_time: '3:00:00'

#Merging or Combining SNEs
SN_nf_combine_sne_queue: 'k2-medpri,k2-fmipr'
SN_nf_combine_sne_cpus: 64
SN_nf_combine_sne_memory: '128 GB'
SN_nf_combine_sne_time: '3:00:00'