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nextflow.config
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nextflow.config
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manifest {
description = 'smMIPS Mutations Detection pipeline implemented using Nextflow'
author = 'Tuhina Srivastava'
nextflowVersion = '20.10.0'
}
params {
input = "/home/pipelines/NextSeq_mutation_detector_leukemia/sample_list.csv"
bedfile = "/home/pipelines/bedfile/06112021_Leukemia_Panel_sorted"
adaptors = "/home/programs/Trimmomatic-0.39/adapters/TruSeq2-PE.fa"
sequences = "/home/pipelines/NextSeq_mutation_detector_leukemia/sequences/"
genome = "/home/reference_genomes/hg19_broad/hg19_all.fasta"
samtools = "/home/programs/samtools-1.7/samtools"
bedtools = "/usr/bin/bedtools"
flt3_bedfile = "/home/pipelines/bedfile/FLT3_pindel"
site1 = "/home/reference_genomes/dbSNPGATK/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf"
site2 = "/home/reference_genomes/dbSNPGATK/dbsnp_138.hg19.vcf"
site3 = "/home/reference_genomes/dbSNPGATK/1000G_phase1.snps.high_confidence.hg19.sites.vcf"
cycle = "500"
ea_utils_path= "/home/programs/ea-utils/clipper"
picard_path = "/home/programs/picard/build/libs/picard.jar"
picard_interval = "/home/pipelines/NextSeq_mutation_detector_leukemia/scripts/leukemia_interval.list"
pear_path = "/home/programs/pear-0.9.10-linux-x86_64/bin/pear"
GATK38_path = "/home/programs/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef/GenomeAnalysisTK.jar"
freebayes_path = "/home/programs/freebayes/bin/freebayes"
platypus_path = "/home/programs/Platypus/bin/Platypus.py"
vardict_path = "/home/programs/VarDictJava/build/install/VarDict/bin"
varscan_path = "/home/programs/VarScan.v2.3.9.jar"
bcftools_path = "/home/programs/bcftools-1.9/bcftools"
strelka_path = "/home/programs/strelka-2.9.2.centos6_x86_64/bin"
NA12878_bam = "/home/reference_genomes/NA12878/NA12878.final.bam"
lofreq_path = "/home/programs/lofreq_star-2.1.4_linux-x86-64/bin/lofreq"
coverview_path = "/home/programs/CoverView-1.4.3"
cava_path = "/home/programs/CAVA/"
somaticseq_path = "/home/miniconda3/bin/somaticseq_parallel.py"
annovarLatest_path= "/home/programs/annovar_latest/annovar/"
bam2pindel= "/home/programs/pindel-master/bam2pindel.pl"
pindel= "/home/programs/pindel-master/"
pindel_config_script = "/home/pipelines/NextSeq_mutation_detector_leukemia/scripts/make_config.sh"
cnvkitRef = "/home/pipelines/NextSeq_mutation_detector_leukemia/scripts/cnvkit_ref_GeneNames/Reference_labelled.cnn"
genome_minimap_getitd = "/home/reference_genomes/hg37_chr/hg37_chr/hg37.fa"
get_itd_path = "/home/programs/GET_ITD_1_5_15/getitd/"
splitvcf_path = "/home/programs/somaticseq-3.6.3/build/lib/somaticseq/vcfModifier/splitVcf.py"
coverview_script_path = "/home/pipelines/mutation_detector_nextflow/scripts/coverview.py"
coverview_report_path = "/home/pipelines/mutation_detector_nextflow/scripts/coverview_report.py"
cava_script_path = "/home/pipelines/mutation_detector_nextflow/scripts/cava.py"
coveragePlot_script = "/home/pipelines/mutation_detector_nextflow/scripts/coverageplot.py"
format_platypus_script = "/home/pipelines/mutation_detector_nextflow/scripts/platypusoutput-format.py"
format_freebayes_script = "/home/pipelines/mutation_detector_nextflow/scripts/freebayesoutput-format.py"
format_vardict_script = "/home/pipelines/mutation_detector_nextflow/scripts/vardictoutput-format.py"
format_combined_script = "/home/pipelines/NextSeq_mutation_detector_leukemia/scripts/combineoutput-format_v2.py"
format_somaticseq_script = "/home/pipelines/NextSeq_mutation_detector_leukemia/scripts/somaticseqoutput-format_v2.py"
format_concat_script = "/home/pipelines/NextSeq_mutation_detector_leukemia/scripts/concat_combine_somatic.py"
format_remove_artefact_script = "/home/pipelines/NextSeq_mutation_detector_leukemia/scripts/remove_artefacts.py"
artefactFile = "/home/pipelines/NextSeq_mutation_detector_leukemia/scripts/artefacts.csv"
format_pindel_script = "/home/pipelines/mutation_detector_nextflow/scripts/pindel_format_csv.py"
merge_csvs_script = "/home/pipelines/NextSeq_mutation_detector_leukemia/scripts/merge-csv_v3.py"
pharma_marker_script = "/home/pipelines/NextSeq_mutation_detector_leukemia/scripts/pharma_markers_v2.py"
pharma_input_xlxs = "/home/pipelines/NextSeq_mutation_detector_leukemia/scripts/For_pharmacogenomics.xlsx"
gene_scatter = "/home/pipelines/NextSeq_mutation_detector_leukemia/scripts/gene_scatter"
pcgr_script_path = "/home/pipelines/NextSeq_mutation_detector_leukemia/scripts/pcgr.sh"
variant_call_path = "/home/pipelines/NextSeq_mutation_detector_leukemia/scripts/variant_callers.py"
vcf_sorter_path = "/home/pipelines/NextSeq_mutation_detector_leukemia/scripts/vcf_sorter.sh"
ensemblid_path = "/home/pipelines/NextSeq_mutation_detector_leukemia/scripts/GENE_IDS/ensemblids.dat"
concat_script_path = "/home/pipelines/NextSeq_mutation_detector_leukemia/scripts/concat_pcgr_cpsr.py"
pcgr_cpsr_script_path = "/home/pipelines/NextSeq_mutation_detector_leukemia/scripts/add_pcgr_cpsr.py"
flash_path="/home/programs/FLASH-1.2.11/flash"
annovar2_path="/home/programs/annovar_latest/annovar/"
combinedCsvFormat_script_path="/home/pipelines/mutation_detector_nextflow/scripts/combined_csv-format.py"
formatLofreq_script_path="/home/pipelines/mutation_detector_nextflow/scripts/lofreqoutput-format.py"
formatMutect_script_path="/home/pipelines/mutation_detector_nextflow/scripts/mutectoutput-format.py"
formatVardict_script_path="/home/pipelines/mutation_detector_nextflow/scripts/vardictoutput-format.py"
KDMdb_script_path="/home/pipelines/mutation_detector_nextflow/scripts/search_KDMmutationDB.py"
mergeAmpliconCsv_path="/home/pipelines/mutation_detector_nextflow/scripts/merge_csv_Amplicon.py"
}
executor {
cpus = 25
}
trace {
enabled = true
file = './Final_Output/pipeline_trace.txt'
fields = 'hash,task_id,name,status,exit,realtime,%cpu,rss'
}