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snakemake_config.yaml
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snakemake_config.yaml
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# MS-GF+ configuration
msgf_path: '/path/to/msgfplus/MSGFPlus.jar'
# Input the mzML files of MS proteomics
ms_datasets:
dataset_1_name:
mzml_dir: 'test_data/ms_dataset_1/mzML'
msgf_config: 'test_data/ms_dataset_1/msgf_config.txt'
dataset_2_name:
mzml_dir: 'test_data/ms_dataset_2/mzML'
msgf_config: 'test_data/ms_dataset_2/msgf_config.txt'
# Input FASTA of protein sequences as reference
protein_fasta: ''
# Input the GTF file processed from RNA-seq
# If no protein sequences input, the GTF file is used to translate protein sequences
RNA_gtf: 'test_data/rna_seq.gtf'
# Predict longest ORFs in transcripts to translate proteins
# Set to false if CDS coordinates are involved in the GTF
predict_ORF: true
# Set to false to include translation products of transcripts annotated/predicted as NMD targets
# NMD prediction rules: 1. > one exon; 2. CDS >= 150nt; 3. lastEJC - stop_codon >= 50nt
discard_NMD: true
# Merge the following canonical references to final protein database
merge_UniProt_protein: true
merge_GENCODE_protein: false
customized_canonical_protein_path: ''
# Canonical protein reference files
# By default, resulted PSMs are searched in UniProt and in GENCODE
UniProt_protein_path: ''
GENCODE_protein_path: ''
# Genome reference and GENCODE annotation files, set path to empty will automatically download the GTF and FASTA to reference_dir
#Default is empty. Set to /path/to/genome.fa to use your own genome.
genome_fasta_path: ''
#Default is empty. Set to /path/to/GENCODE.gtf to use your own annotation.
GENCODE_gtf_path: ''
genome_fasta_path: ''
# Default references url
# If the reference files above are not given, the following will be downloaded and parsed to reference_dir
UniProt_protein_url: 'https://ftp.uniprot.org/pub/databases/uniprot/previous_major_releases/release-2021_04/knowledgebase/uniprot_sprot-only2021_04.tar.gz'
GENCODE_protein_url: 'https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_39/gencode.v39.pc_transcripts.fa.gz'
genome_fasta_url: 'https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_39/GRCh38.primary_assembly.genome.fa.gz'
GENCODE_gtf_url: 'https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_39/gencode.v39.annotation.gtf.gz'
# Working directory
reference_dir: 'test_output/protein_db'
log_dir: 'test_output/log'
work_dir: 'test_output/work_dir'
results_dir: 'test_output/results'
visualization_dir: 'test_output/visualization'
# Percolator configuration
train_fdr: 0.05
test_fdr: 0.05
qvalue_cutoff: 0.05
# Resource allocation
msgf_mem_gb: 48
msgf_threads: 8
msgf_time_hr: 12
percolator_mem_gb: 16
percolator_threads: 8
percolator_time_hr: 12
# Decoy database construction method, if both are on, will first reverse each sequence and then shuffle each sequence
reverse: false
shuffle: true
# Visualize novel peptides, RNA_gtf must be provided
enable_visualization: true
visualization_mem_gb: 8
visualization_time_hr: 12
# Predict gene level expression by EM algorithm
report_intensity: true
predict_gene_by_intensity: true
predict_gene_by_PSM_count: true
scripts_dir: 'scripts'
conda_wrapper: conda_wrapper