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nextflow.config
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nextflow.config
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// your workflow parameters
params {
resultsDir = "./results/"
// GET_METADATA parameters
taxonId = "562"
limitSearch = "0"
removeRun = '"SRR13894889"'
max_sra_bytes = "55000000000"
dateMin = "2017-05-01"
dateMax = "2017-05-31"
// Genome files
genome.reference = "testdata/genome/Escherichia_coli_str_k_12_substr_mg1655_gca_000005845.ASM584v2.dna.chromosome.Chromosome.fa"
genome.annotation = "testdata/genome/Escherichia_coli_str_k_12_substr_mg1655_gca_000005845.ASM584v2.53.gtf"
// STAR parameters
star.sjdbOverhang = "100"
star.genomeSAindexNbases = "10"
star.alignIntronMax = "1"
star.limitBAMsortRAM = "2342750981"
star.outBAMsortingBinsN = "50"
// featureCounts parameters
featureCounts.type.feature = "exon"
featureCounts.type.attribute = "gene_id"
// freebayes parameters
freebayes.ploidy = "1"
freebayes.args = ""
// bcftools parameters
bcftools.filter_vcf.args = 'QUAL>20 && TYPE="snp"'
// SALMON_INDEX parameters
salmon.index.args = ""
// SALMON_QUANT parameters
salmon.quant.libtype = "A"
// salmon.quant.args = "--writeUnmappedNames"
// SUMMARIZE_TO_GENE parameters
summarize_to_gene.metadata = "testdata/test-data/metadata/metadata.csv"
summarize_to_gene.quant.dir = "testdata/test-data/salmon-quant"
summarize_to_gene.counts_from_abundance = "no"
// GET_HEG_LEG parameters
get_heg_leg.proportion = 0.1
get_heg_leg.permutations = 1000
get_heg_leg.output.heg = "heg-TrID.csv"
get_heg_leg.output.leg = "leg-TrID.csv"
// GET_HEG_LEG_FASTA parameters
mut_fasta = "testdata/test-data/mut-transcriptome"
get_heg_leg_fasta.heg_scores = ""
get_heg_leg_fasta.leg_scores = ""
// GET_CU_FREQUENCIES parameters
get_cu_frequencies.heg_fasta_dir = "testdata/test-data/heg-mut-transcriptome"
get_cu_frequencies.leg_fasta_dir = "testdata/test-data/leg-mut-transcriptome"
get_cu_frequencies.protein_fasta_dir = "results/protein-mut-transcriptome"
get_cu_frequencies.tax_id = "83333"
get_cu_frequencies.cocoputs_counts = "testdata/get-cu-frequencies/cocoputs-83333-codon-counts.csv"
// GET_CU_FIGURES parameters
get_cu_figures.aa_property_table = "testdata/figure-data/aa-properties.csv"
// GET_KO_ID parameters
get_ko_id.org = "eco"
// CORDON_CODON_USAGE_ANALYSIS
coRdon.cub_statistic = "MILC"
coRdon.len_threshold = "80"
// GET_TOP_GENES parameters
top.genes.id = "testdata/datasets/txi-topGenes2trID.txt"
// metadata
//metadata = "testdata/test-data/metadata/metadata-delim.csv"
metadata = "testdata/vcfr-test/metadata-delim.csv"
// STRAIN_HEG_CAT_PLOT parameters
real.txi = "results/real-data/txi-summarized-experiment.rds"
real.metadata = "results/real-data/metadata.csv"
strain_heg_cat_plot.fdr = "0.01"
strain_heg_cat_plot.num_strains = "10"
// GET_STRAIN_CAT_PLOT parameters
get_strain_cat_plot.tax_names = "testdata/cat-analysis/ncbi-ecoli-taxdump.csv"
get_strain_cat_plot.heg_scores = "testdata/cat-analysis/heg-scores.csv"
get_strain_cat_plot.leg_scores = "testdata/cat-analysis/leg-scores.csv"
get_strain_cat_plot.num_strains = "10"
get_strain_cat_plot.fdr = "0.01"
// VARIANT_ANALYSIS parameters
vcf_dir = "testdata/test-data/filtered-vcf"
gff = "testdata/genome/Escherichia_coli_str_k_12_substr_mg1655_gca_000005845.ASM584v2.55.chromosome.Chromosome.gff3.gz"
// DEBUG_BCFTOOLS parameters
debug_bcftools.metadata = "testdata/debug-bcftools/metadata/metadata.csv"
debug_bcftools.vcf = "testdata/debug-bcftools/vcf"
// CORRECT_SNV parameters
correct_snv.bam = "testdata/test-data/bams"
// GET_PCA parameters
get_pca.txi = "results/data/dataset/txi-summarized-experiment.rds"
get_pca.metadata = "results/data/metadata/norm_metadata.csv"
// RANK_GENES parameters
rank_genes.fdr = "0.01"
// MERGE_VCF parameters
//vcf = "testdata/test-data/filtered-vcf"
//merge_vcf.vcf_dir = "testdata/test-data/filtered-vcf/*.vcf.gz"
merge_vcf.vcf_dir = "testdata/vcfr-test/vcf-test/*.vcf.gz"
vcf = "testdata/vcfr-test/vcf-test"
// VCFR_QC parameters
vcfr_qc.merged_vcf = "results/merged-vcf/merged.vcf"
// GET_VCF_STATS parameters
get_vcf_stats.merged_vcf = "testdata/vcfr-test/merged-vcf/merged.vcf"
// PLOT_VCF_STATS parameters
plot_vcf_stats.main_title = "'Escherichia coli merged samples'"
// STRAIN_CU_HEATMAP parameters
strain_cu_heatmap.metadata = "testdata/test-data/metadata/metadata.csv"
strain_cu_heatmap.fasta = "testdata/test-data/heg-mut-transcriptome"
strain_cu_heatmap.width = "15"
strain_cu_heatmap.height = "15"
// ANNOTATE_VCF parameters
annotate_vcf.dir = "results/mut-gene-count"
// MERGE_VCF parameters
bcftools_view.merged_vcf = "test.vcf"
plot_vcf.merged_vcf = "testdata/merged-vcf/subset-merged-vcf.vcf"
// SUMMARISE_CODON_COUNTS parameters
summarise_cc.codon_counts_csv = "testdata/codon-counts/protein-cc-subset.csv"
// PLOT_MUTATION_CIRCOS parameters
mutation_freq_data = "testdata/circos-test/mutation-frequency-data-subset.csv"
gene_tpm_scores = "testdata/circos-test/chisq-results.csv"
}
// include basic process configuration options
includeConfig 'conf/base.config'