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full.config
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full.config
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// change these paths to lead to your files
params {
riboseq_reads = "${projectDir}/../data/muscle_samples/*.fastq.gz"
proteomics_reads = "${projectDir}/../data/nitish_new_muscle_proteomics/*.mzML"
gtf = "${projectDir}/../data/normal_and_rnacentral_gtf_for_nitish_data/Mus_musculus.GRCm39.105_and_rnacentral.gtf"
other_RNAs_sequence = "${projectDir}/../data/ribosomal_DNA/Mus_musculus_rDNA_complete_repeating_unit.fa"
genome = "${projectDir}/../data/Mus_musculus.GRCm39/Mus_musculus.GRCm39.dna.primary_assembly.fa"
swissprot = "${projectDir}/../data/swiss-prot-2022_03/swissprot_2022_03_only_mouse.fasta"
}
// the following parameters are from the actual tools run by the pipeline
// only change these values if you know what you are doing
params {
cut = "5"
minimum_length = 20
clip_reads_args = "-v -n -c -z -a AAAAAAAAAA -l 20"
trim_reads_args = "-v -l 20 -t 20 -z -Q 33"
filter_reads_args = "-v -q 20 -p 90 -z -Q 33"
fastq_to_fasta_args = "-v -n -r"
segemehl_args = "--silent --accuracy 90 --threads 25"
star_threads = 24
check_periodicity_codnum = 100
ribotish_quality_args = "--th 0.4 --nom0"
//ribotish_predict_args = "--alt --transprofile TRANSPROFILE --seq --aaseq -v --longest" // --longest/""
ribotish_predict_args = "-v --longest" // --longest/""
workspace = "${projectDir}/workspace"
fragger_mode = "nonspecific" // open/closed/nonspecific/glyco
peptideprophet_args = "--combine --decoy rev_ --ppm --accmass --expectscore --decoyprobs --nonparam"
philosopher_filter_args = "--psm 0.05 --ion 0.05 --pep 0.05 --prot 1 --picked --tag rev_"
}
// these paths can be changed if you want your output files to be stored elsewhere on your system
params {
annotate_dir = "results/full/annotate"
riboseq_dir = "results/full/riboseq"
ribotish_dir = "results/full/ribotish"
philosopher_dir = "results/full/philosopher"
qc_dir = "results/full/qc"
map_dir = "results/full/map"
reads_dir = "results/full/prepare_reads"
log_dir = "logs/full"
}
// do not change these params
params {
run_mode = "full"
}