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nextflow.config
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nextflow.config
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profiles {
standard {
docker {
enabled = true
envWhitelist = "SLURM_CPUS_ON_NODE"
runOptions = '-v "$TMPDIR":"$TMPDIR"' // For compatibility with the parallel command called by Tb-Profiler
}
}
docker {
docker {
enabled = true
envWhitelist = "SLURM_CPUS_ON_NODE"
runOptions = '-v "$TMPDIR":"$TMPDIR"' // For compatibility with the parallel command called by Tb-Profiler
}
}
podman {
podman {
enabled = true
envWhitelist = "SLURM_CPUS_ON_NODE"
runOptions = '-v "$TMPDIR":"$TMPDIR"' // For compatibility with the parallel command called by Tb-Profiler
}
}
singularity {
singularity {
enabled = true
envWhitelist = "SLURM_CPUS_ON_NODE"
runOptions = '-B "$TMPDIR"' // For compatibility with the parallel command called by Tb-Profiler
autoMounts = true
}
}
}
process {
executor = "slurm"
clusterOptions = "-A walter --partition notchpeak -N 1 --time=10:00:00"
errorStrategy = "ignore"
withLabel: trimgalore {
container = "ksw9/mtb-call:trimgalore"
}
withLabel: kraken2 {
container = "ksw9/mtb-call:kraken2"
}
withLabel: mapping {
container = "ksw9/mtb-call:mapping"
}
withLabel: amr {
container = "ksw9/mtb-call:amr"
}
withLabel: tb_profiler {
container = "ksw9/mtb-call:tbprofiler"
// errorStrategy set to "retry" to deal with random failures of TB-Profiler
errorStrategy = "retry"
maxRetries = 10
}
withLabel: variantcalling {
container = "ksw9/mtb-call:variantcalling"
}
withLabel: makesummary {
container = "ksw9/mtb-call:trimgalore"
}
}
params {
// Main files/directories
// N.B. All paths are relative to resources_dir
resources_dir = "/uufs/chpc.utah.edu/common/home/walter-group2/tb/mtb-call2/resources"
reads_list = "input/goig.tsv"
kraken_database_path = "kraken_db"
reference_fasta_path = "refs/H37Rv.fasta"
reference_fasta_index_path = "refs/H37Rv.fasta.fai"
bwa_index_path = "bwa_index"
bowtie_index_path = "bowtie2_index"
bowtie_index_prefix = "H37Rv"
gatk_dictionary_path = "gatk_dictionary/H37Rv.dict"
bed_path = "bed/H37Rv_ppe.bed.gz"
bed_index_path = "bed/H37Rv_ppe.bed.gz.tbi"
vcf_header = "bed/ppe_hdr.txt"
snpeff_dir = "snpEff"
snpeff_db = "Mycobacterium_tuberculosis_h37rv"
snpeff_datapath = "snpEff/data"
snpeff_config = "snpEff/snpEff.config"
// Main variables
mapper = "bwa"
run_lofreq = true
seq_platform = "illumina"
library = "library1"
depth_threshold = 5
qual_threshold = 20
ploidy = 1
nextseq = false
nextseq_qual_threshold = 20
variants_only = true
}