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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phac-nml/mikrokondo Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
// Index creation output file
output_idx_name = null
// List all allowed platforms
opt_platforms {
// ! WARNING if these are ever spelt wrong you get esoteric errors...
illumina = "illumina"
ont = "nanopore"
pacbio = "pacbio"
hybrid = "hybrid" // assumes illumina and long reads
}
flye_read_type = "hq" // options are hq, corr or raw
platform = params.opt_platforms.illumina
long_read_opt = params.opt_platforms.ont
nanopore_chemistry = null
run_kraken = false // Run kraken if true or mash screen on contigs if false
hybrid_unicycler = false // run alternative assembly workflow
// Filtering options
min_reads = 1000 // The minimum number of reads needed for a sample to continue through the pipeline
// Sub sampling options
target_depth = 100
validate_params = true
show_hidden_params = false
validationS3PathCheck = true
validationShowHiddenParams = false
validationSchemaIgnoreParams = 'top_hit_method,abricate,locidex,assembly_status,bakta,bandage,checkm,chopper,contigs_too_short,coreutils,coverage_calc_fields,ectyper,fastp,fastqc,filtered_reads,flye,kat,kleborate,kraken,kraken_bin,kraken_species,lissero,mash,mash_meta,medaka,minimap2,mlst,mobsuite_recon,opt_platforms,pilon,pilon_iterative,pointfinder_db_tag,python3,QCReport,QCReport-fields,QCReportFields,quast,racon,raw_reads,report_aggregate,r_contaminants,samtools,seqkit,seqtk,seqtk_size,shigeifinder,sistr,spades,spatyper,staramr,subtyping_report,top_hit_species,unicycler'
validationFailUnrecognisedParams = false // for the qcreport fields
// SKIP options
// TODO need to add constants section
// TODO investigate usage of template scripts to replace mash modules
skip_report = false
skip_raw_read_metrics = false
skip_version_gathering = false
skip_subtyping = false
skip_bakta = true
skip_abricate = false
skip_checkm = false
skip_depth_sampling = false // TODO have it mentioned that this should be turned off for metagenomic runs
skip_ont_header_cleaning = true // TODO an awk script can likely replace this and be much faster at what it does...
skip_polishing = false // TODO make it clear this does not apply to Hybrid assembly
skip_species_classification = false
skip_mlst = false
skip_mobrecon = false
skip_staramr = false
skip_metagenomic_detection = false // Skip classifying if sample is metagenomic
skip_allele_calling = false
skip_length_filtering_contigs = false
metagenomic_run = false // Label all samples as
// Datasets
dehosting_idx = null // mm2 index
mash_sketch = null // Make sure comments are formatted as taxonomic strings
bakta_db = null
kraken2_db = null
staramr_db = null // Recommended usage is to use the default database in the container
// FastP parameters
fp_average_quality = 25
fp_cut_tail_mean_quality = 15
fp_cut_tail_window_size = 4
fp_complexity_threshold = 20
fp_qualified_phred = 15
fp_unqualified_percent_limit = 40
fp_polyg_min_len = 10
fp_polyx_min_len = 10
fp_illumina_length_min = 35
fp_illumina_length_max = 400
fp_single_end_length_min = 1000 // Affects nanopore only
fp_dedup_reads = false
// Bakta Parmeters
ba_min_contig_length = 200
// Quast parameters
qt_min_contig_length = 1000
// Mash
mh_min_kmer = 10
// ECTyper Parameters
ec_opid = 90 // Minimum percent identity to determine O antigens prescence
ec_opcov = 90 // Minimum percent coverage of O antigen
ec_hpid = 95 // Miniumum percent identity to determine H antigens prescence
ec_hpcov = 50 // Minimum percent coverage of H antigen
ec_enable_verification = true // Enable species verification in ECTyper
// SISTR parameters
sr_full_cgmlst = true // Use full set of cgMLST alleles which can include highly similar alleles
// Locidex Options
lx_min_evalue = 0.0001
lx_min_dna_len = 1
lx_min_aa_len = 1
lx_max_dna_len = 10000000
lx_max_aa_len = 10000000
lx_min_dna_ident = 80.0
lx_min_aa_ident = 80.0
lx_min_dna_match_cov = 80.0
lx_min_aa_match_cov = 80.0
lx_max_target_seqs = 10
lx_extraction_mode = "raw"
lx_report_mode = "normal"
lx_report_prop = "locus_name"
lx_report_max_ambig = 0
lx_report_max_stop = 0
// Overide an allele calling scheme, this will be applied globally if auto selection is not opted for
allele_scheme = null
// Boilerplate options
outdir = null
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
// If a param in camel case is present nextflow automatically creates a kebab case parameter as well
stage_in_mode = 'symlink'
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_description = null
config_profile_contact = null
config_profile_url = null
config_profile_name = null
// use slurm executor
// TODO add in max runtime for jobs, as to not run up cloud, local or cluster resources
slurm_p = false
slurm_profile = ""
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '2000.GB'
max_cpus = 16
max_time = '240.h'
abricate {
singularity = "https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1"
docker = "quay.io/biocontainers/abricate:1.0.1--ha8f3691_1"
args = { "" }
report_tag = "Abricate"
header_p = true
}
raw_reads {
high_precision = false // Makes things really slow
report_tag = "RawReadSummary"
}
// coreutils e.g. cat
coreutils {
singularity = "https://depot.galaxyproject.org/singularity/coreutils%3A8.31--h14c3975_0"
docker = 'quay.io/biocontainers/coreutils:8.31--h14c3975_0'
}
// Python container, May switch for pypy3
python3 {
singularity = "quay.io/biocontainers/staramr:0.10.0--pyhdfd78af_0"
docker = "quay.io/biocontainers/staramr:0.10.0--pyhdfd78af_0"
}
seqtk {
singularity = 'https://depot.galaxyproject.org/singularity/seqtk%3A1.4--he4a0461_1'
docker = 'quay.io/biocontainers/seqtk:1.4--he4a0461_1'
seed = 42
reads_ext = ".sampled.fastq.gz"
assembly_fastq = ".fastq.gz"
report_tag = "Seqtk"
}
seqtk_size {
singularity = 'https://depot.galaxyproject.org/singularity/seqtk%3A1.4--he4a0461_1'
docker = 'quay.io/biocontainers/seqtk:1.4--he4a0461_1'
report_tag = "SeqtkBaseCount"
}
locidex {
// awaiting singluarity image build
//singularity = "https://depot.galaxyproject.org/singularity/locidex%3A0.1.1--pyhdfd78af_1"
singularity = "quay.io/biocontainers/locidex:0.1.1--pyhdfd78af_1"
docker = "quay.io/biocontainers/locidex:0.1.1--pyhdfd78af_1"
min_evalue = params.lx_min_evalue
min_dna_len = params.lx_min_dna_len
min_aa_len = params.lx_min_aa_len
max_dna_len = params.lx_max_dna_len
max_aa_len = params.lx_max_aa_len
min_dna_ident = params.lx_min_dna_ident
min_aa_ident = params.lx_min_aa_ident
min_dna_match_cov = params.lx_min_dna_match_cov
min_aa_match_cov = params.lx_min_aa_match_cov
max_target_seqs = params.lx_max_target_seqs
extraction_mode = params.lx_extraction_mode
report_mode = params.lx_report_mode
report_prop = params.lx_report_prop
report_max_ambig = params.lx_report_max_ambig
report_max_stop = params.lx_report_max_stop
extracted_seqs_suffix = ".extracted.seqs.fasta.gz"
seq_store_suffix = ".seq_store.json.gz"
gbk_suffix = ".gbk.gz"
extraction_dir = "extracted"
report_suffix = ".profile.mlst.json.gz"
schemes {
salmonella {
search = params.QCReport.salmonella
db = null
}
}
}
// FASTP options
fastp {
fastq_ext = ".trimmed.fastq.gz"
singularity = 'https://depot.galaxyproject.org/singularity/fastp%3A0.23.2--hb7a2d85_2'
docker = 'quay.io/biocontainers/fastp:0.23.2--hb7a2d85_2'
html_ext = ".html"
json_ext = ".json"
report_tag = "FastP"
average_quality_e = params.fp_average_quality // The -e option in fastp for if the average quality is less than specified then read/read-pair is discarded
cut_tail_mean_quality = params.fp_cut_tail_mean_quality
cut_tail_window_size = params.fp_cut_tail_window_size // default is 4
complexity_threshold = params.fp_complexity_threshold // FastP default is 30 not 20
qualified_quality_phred = params.fp_qualified_phred // min quality for a read to contain
unqualified_percent_limit = params.fp_unqualified_percent_limit // if the minimum quality of a read is below 10 that read is discarded
polyg_min_len = params.fp_polyg_min_len
polyx_min_len = params.fp_polyx_min_len
illumina_length_min = params.fp_illumina_length_min
illumina_length_max = params.fp_illumina_length_max
single_end_length_min = params.fp_single_end_length_min
dedup_reads = params.fp_dedup_reads
// -c is used to apply overlap analysis and cut out out adapters
args {
illumina = "--overrepresentation_analysis --trim_poly_g --poly_g_min_len ${params.fastp.polyg_min_len} --trim_poly_x --poly_x_min_len ${params.fastp.polyx_min_len} --cut_tail --cut_tail_window_size ${params.fastp.cut_tail_window_size} --cut_tail_mean_quality ${params.fastp.cut_tail_mean_quality} --low_complexity_filter --complexity_threshold ${params.fastp.complexity_threshold} --average_qual ${params.fastp.average_quality_e} --qualified_quality_phred ${params.fastp.qualified_quality_phred} --unqualified_percent_limit ${params.fastp.unqualified_percent_limit} --length_limit ${params.fastp.illumina_length_max} --length_required ${params.fastp.illumina_length_min} --detect_adapter_for_pe"
single_end = "--overrepresentation_analysis -Q --length_required ${params.fastp.single_end_length_min}"
}
report_exclude_fields = ["content_curves", "quality_curves", "mean", "kmer_count", "histogram", "overrepresented_sequences"]
}
// Nanofilter options
chopper {
singularity = 'https://depot.galaxyproject.org/singularity/chopper%3A0.5.0--hd03093a_0'
quality = 0
minlength = 100
fastq_ext = ".fastq.gz"
}
// Flye options
// TODO figure out if --keep-haplotypes should be enabled
flye {
// TODO add in arg for data type in flye
nanopore {
raw = "--nano-raw"
corr = "--nano-corr"
hq = "--nano-hq"
}
pacbio {
raw = "--pacbio-raw"
corr = "--pacbio-corr"
hq = "--pacbio-hifi" // TODO all reads are marked as hifi
}
singularity = 'https://depot.galaxyproject.org/singularity/flye:2.9--py39h6935b12_1'
docker = 'quay.io/biocontainers/flye:2.9.2--py39h6935b12_0'
fasta_ext = ".fasta.gz"
gfa_ext = ".gfa.gz"
gv_ext = ".gv.gz"
txt_ext = ".txt"
log_ext = ".log"
json_ext = ".json"
polishing_iterations = 1
args = { "--iterations ${params.flye.polishing_iterations}" } // this is normlly configured through task.ext.args... but idk how I feel about that yet
}
// SPADES options
spades {
singularity = 'https://depot.galaxyproject.org/singularity/spades:3.15.5--h95f258a_1'
docker = 'quay.io/biocontainers/spades:3.15.5--h95f258a_1'
outdir = "assembly"
scaffolds_ext = ".scaffolds.fasta.gz"
contigs_ext = ".contigs.fasta.gz"
transcripts_ext = ".transcripts.fasta.gz"
gene_clusters_ext = ".gene_clusters.fasta.gz"
assembly_graphs_ext = ".assembly.gfa.gz"
log_ext = ".log"
}
// Fastqc options
fastqc {
html_ext = ".html"
zip_ext = ".zip"
}
// TODO add to docs
seqkit {
singularity = 'https://depot.galaxyproject.org/singularity/seqkit:2.2.0--h9ee0642_0'
docker = 'quay.io/biocontainers/seqkit:2.2.0--h9ee0642_0'
report_ext = ".tsv"
fasta_ext = ".filtered.fasta.gz"
filter_field = "max_len"
report_tag = "Seqkit_stats"
header_p = true
}
// QUAST args
quast{
singularity = 'https://depot.galaxyproject.org/singularity/quast%3A5.2.0--py39pl5321h4e691d4_3' // not all Quast containers work, might get file system error with BWA, if issue persists reads can be not passed to the module instead
docker = 'quay.io/biocontainers/quast:5.2.0--py39pl5321h4e691d4_3'
suffix = "quast"
report_base = "report"
report_prefix = "transposed_"
report_ext = ".tsv"
report_tag = "QUAST"
min_contig_length = params.qt_min_contig_length
contigs_field = "# contigs"
// need to add a --min-contig args to set to 0 as at 500 currently add --report-all-metrics
// also need to see if a sam can be published from quast
args = { "--min-contig ${params.quast.min_contig_length} --report-all-metrics" }
header_p = true
}
checkm {
// TODO add to trouble shooting if checkm fails and provides EOF errors, to try changing the container
singularity = 'https://depot.galaxyproject.org/singularity/checkm-genome%3A1.2.2--pyhdfd78af_1'
docker = 'quay.io/biocontainers/checkm-genome:1.2.2--pyhdfd78af_1'
alignment_ext = ".genes.aln"
results_ext = ".results.txt"
tsv_ext = ".tsv"
folder_name = "checkm"
gzip_ext = ".gz"
lineage_ms = "lineage.ms"
report_tag = "CheckM"
header_p = true
}
// Kraken args
kraken {
singularity = 'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0'
docker = 'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:941789bd7fe00db16531c26de8bf3c5c985242a5-0'
db = params.kraken2_db
classified_suffix = "classified"
unclassified_suffix = "unclassified"
report_suffix = "report"
output_suffix = "output"
tophit_level = "S" // level to select the samples top-hit based on kraken2
save_output_fastqs = false
save_reads_assignments = true
run_kraken_quick = false
report_tag = "KrakenReport"
header_p = false
headers = ["PercentID", "FragmentsRecovered", "FragmentsAssignmentTaxon", "RankCode"]
}
mlst {
singularity = "https://depot.galaxyproject.org/singularity/mlst:2.19.0--hdfd78af_1"
docker = "quay.io/biocontainers/mlst:2.19.0--hdfd78af_1"
args = ""
tsv_ext = ".tsv"
json_ext = ".json"
report_tag = "SevenGeneMLSTReport"
}
mash {
singularity = "https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1"
docker = 'quay.io/biocontainers/mash:2.3--he348c14_1'
// going forward labeled with _ext include '.'
mash_ext = ".screen" //TODO refactor out of utility workflow
output_reads_ext = ".reads.screen"
output_taxa_ext = ".taxa.screen"
output_dir = "contamination"
mash_sketch = params.mash_sketch
sketch_ext = ".msh"
json_ext = ".json"
sketch_kmer_size = 21 // defualt param in mash
min_kmer = params.mh_min_kmer
final_sketch_name = "GTDB_sketch"
report_tag = "Mash"
header_p = false
headers = ["identity", "Shared Hashes", "Median Multiplicity", "P-Value", "Query ID", "Query Note"]
}
mash_meta {
report_tag = "MashMeta"
}
top_hit_species {
report_tag = "SpeciesTopHit"
}
top_hit_method {
report_tag = "IdentificationMethod"
}
r_contaminants {
// container contains minimap2 and samtools
singularity = "https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:3161f532a5ea6f1dec9be5667c9efc2afdac6104-0"
docker = "quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:3161f532a5ea6f1dec9be5667c9efc2afdac6104-0"
phix_fa = ""
homo_sapiens_fa = ""
pacbio_mg = ""
output_ext = ".cleaned.fastq.gz"
mega_mm2_idx = params.dehosting_idx
mm2_illumina = "-x sr" // ax outputs sam
mm2_pac = "-x map-pb"
mm2_ont = "-x map-ont"
mm2_output_ext = ".sam"
samtools_output_ext = ".fastq"
samtools_singletons_ext = ".singleton.fq"
samtools_output_suffix = "deconned"
output_ext = "${samtools_output_ext}.gz"
output_dir = "${params.mash.output_dir}/deconned_reads"
}
minimap2 {
// for creation of indices from assemblies
singularity = params.r_contaminants.singularity
docker = params.r_contaminants.docker
index_outdir = "indices"
index_ext = ".idx"
mapped_paf_ext = ".paf"
mapped_sam_ext = ".sam"
mapped_outdir = "mapped"
}
samtools {
singularity = params.r_contaminants.singularity
docker = params.r_contaminants.docker
bam_ext = ".bam"
bai_ext = ".bai"
}
racon {
singularity = 'https://depot.galaxyproject.org/singularity/racon:1.4.20--h9a82719_1'
docker = 'quay.io/biocontainers/racon:1.4.20--h9a82719_1'
consensus_suffix = "_assembly_consensus.fasta"
consensus_ext = ".fasta.gz"
outdir = "polished"
}
pilon {
singularity = 'https://depot.galaxyproject.org/singularity/pilon%3A1.24--hdfd78af_0'
docker = 'quay.io/biocontainers/pilon:1.24--hdfd78af_0'
outdir = "pilon"
fasta_ext = ".fasta.gz"
fasta_outdir = "fasta"
vcf_ext = ".vcf"
vcf_outdir = "vcf"
changes_ext = ".changes"
changes_outdir = "changes"
max_memory_multiplier = 3
}
pilon_iterative {
singularity = 'docker.io/mwells14/pilonpolisher:0.0.1' // Docker containers will be converted to singularity
docker = 'docker.io/mwells14/pilonpolisher:0.0.1'
outdir = "pilon"
fasta_ext = ".fasta.gz"
fasta_outdir = "fasta"
vcf_ext = ".vcf"
vcf_outdir = "vcf"
bam_ext = ".bam"
bai_ext = ".bai"
changes_ext = ".changes"
changes_outdir = "changes"
max_memory_multiplier = 3 // how much memory is increased after each run failure
max_polishing_illumina = 3
max_polishing_pacbio = 4
max_polishing_nanopore = 10
}
medaka {
singularity = 'https://depot.galaxyproject.org/singularity/medaka%3A1.8.0--py38hdaa7744_0'
docker = 'quay.io/biocontainers/medaka:1.8.0--py38hdaa7744_0'
model = params.nanopore_chemistry
fasta_ext = ".fa.gz"
outdir = "medaka"
batch_size = 5
}
unicycler {
singularity = 'https://depot.galaxyproject.org/singularity/unicycler%3A0.5.0--py38h3b68952_2'
docker = 'quay.io/biocontainers/unicycler:0.5.0--py38h3b68952_2'
scaffolds_ext = ".scaffolds.fa.gz"
assembly_ext = ".assembly.gfa.gz"
log_ext = ".unicycler.log"
outdir = "unicycler"
mem_modifier = 1000 // overly large number to provide more memory for unicycler
threads_increase_factor = 1
}
mobsuite_recon {
singularity = 'https://depot.galaxyproject.org/singularity/mob_suite%3A3.0.3--pyhdfd78af_0'
docker = 'quay.io/biocontainers/mob_suite:3.0.3--pyhdfd78af_0'
args = { "" }
fasta_ext = ".fasta"
results_ext = ".txt"
mob_results_file = "mobtyper_results.txt"
contig_report = "contig_report.txt"
report_tag = "MobRecon"
header_p = true
}
staramr {
singularity = "quay.io/biocontainers/staramr:0.10.0--pyhdfd78af_0"
docker = "quay.io/biocontainers/staramr:0.10.0--pyhdfd78af_0"
point_finder_db_default = null
db = null
tsv_ext = ".tsv"
txt_ext = ".txt"
xlsx_ext = ".xlsx"
args = { "" }
// Approved point finder databases
point_finder_dbs = ['salmonella', 'campylobacter', 'enterococcus_faecalis',
'enterococcus_faecium', 'escherichia_coli', 'helicobacter_pylori']
report_tag = "StarAMR"
header_p = true
}
pointfinder_db_tag {
report_tag = "PointfinderDB"
}
bakta {
// TODO verify bakta version in scripts so that greater than 1.8 exists for force options
singularity = 'https://depot.galaxyproject.org/singularity/bakta%3A1.8.1--pyhdfd78af_0'
docker = 'quay.io/biocontainers/bakta:1.8.1--pyhdfd78af_0'
db = params.bakta_db
output_dir = "bakta"
embl_ext = ".embl"
faa_ext = ".faa"
ffn_ext = ".ffn"
fna_ext = ".fna"
gbff_ext = ".gbff"
gff_ext = ".gff3"
threads = 12 // default number of threads, more is not always better
hypotheticals_tsv_ext = ".hypotheticals.tsv"
hypotheticals_faa_ext = ".hypotheticals.faa"
tsv_ext = ".tsv"
txt_ext = ".txt"
min_contig_length = params.ba_min_contig_length
args = { "" }
}
bandage {
singularity = 'https://depot.galaxyproject.org/singularity/bandage:0.8.1--hc9558a2_2'
docker = 'quay.io/biocontainers/bandage:0.8.1--hc9558a2_2'
svg_ext = ".svg"
outdir = "bandage"
}
subtyping_report {
report_tag = "Subtyping"
}
ectyper {
singularity = 'https://depot.galaxyproject.org/singularity/ectyper:1.0.0--pyhdfd78af_1'
docker = 'quay.io/biocontainers/ectyper:1.0.0--pyhdfd78af_1'
log_ext = ".log"
tsv_ext = ".tsv"
txt_ext = ".txt"
opid = params.ec_opid
opcov = params.ec_opcov
hpid = params.ec_hpid
hpcov = params.ec_hpcov
verify = params.ec_enable_verification ? "--verify" : ""
args = { "${params.ectyper.verify} -opid ${params.ectyper.opid} -opcov ${params.ectyper.opcov} -hpid ${params.ectyper.hpcov} -hpcov ${params.ectyper.hpcov}" }
report_tag = "ECTyper${params.subtyping_report.report_tag}"
header_p = true
}
kleborate {
singularity = 'https://depot.galaxyproject.org/singularity/kleborate:2.1.0--pyhdfd78af_1'
docker = 'quay.io/biocontainers/kleborate:2.1.0--pyhdfd78af_1'
txt_ext = ".results.txt"
report_tag = "Kleborate${params.subtyping_report.report_tag}"
header_p = true
}
spatyper {
// TODO figure out what repeats input is
singularity = 'https://depot.galaxyproject.org/singularity/spatyper:0.3.3--pyhdfd78af_3'
docker = 'quay.io/biocontainers/spatyper:0.3.3--pyhdfd78af_3'
tsv_ext = ".tsv"
report_tag = "SpaTyper${params.subtyping_report.report_tag}"
header_p = true
repeats = null
repeat_order = null
}
sistr {
singularity = "https://depot.galaxyproject.org/singularity/sistr_cmd:1.1.1--pyh864c0ab_2"
docker = 'quay.io/biocontainers/sistr_cmd:1.1.1--pyh864c0ab_2'
tsv_ext = ".tab"
allele_fasta_ext = ".allele.fasta"
allele_json_ext = ".allele.json"
cgmlst_ext = ".cgmlst.csv"
full_cgmlst = params.sr_full_cgmlst
report_tag = "SISTR${params.subtyping_report.report_tag}"
header_p = true
}
lissero {
singularity = 'https://depot.galaxyproject.org/singularity/lissero:0.4.9--py_0'
docker = 'quay.io/biocontainers/lissero:0.4.9--py_0'
tsv_ext = ".tsv"
report_tag = "LISSERO${params.subtyping_report.report_tag}"
header_p = true
}
shigeifinder {
container_version = '1.3.2' // update version info with containers as it is not included in shigeifinder
singularity = 'https://depot.galaxyproject.org/singularity/shigeifinder:1.3.2--pyhdfd78af_0'
docker = 'quay.io/biocontainers/shigeifinder:1.3.2--pyhdfd78af_0'
tsv_ext = ".tsv"
report_tag = "Shigeifinder${params.subtyping_report.report_tag}"
header_p = true
}
//shigatyper {
// singularity = 'https://depot.galaxyproject.org/singularity/shigatyper%3A2.0.1--pyhdfd78af_0'
// docker = 'quay.io/biocontainers/shigatyper:2.0.1--pyhdfd78af_0'
// tsv_ext = ".tsv"
// report_tag = "ShigaTyper${params.subtyping_report.report_tag}"
// //report_tag = params.subtyping_report.report_tag
// header_p = true
//}
coverage_calc_fields {
//bp_field = params.seqtk_size.report_tag // Trimmed base count size
bp_field = [params.raw_reads.report_tag, "combined", "total_bp"]
fixed_cov = "FixedGenomeSizeDepth"
auto_cov = "DetectedGenomeSizeDepth"
}
assembly_status {
report_tag = "AssemblyCompleted"
}
contigs_too_short {
report_tag = "MaxContigToShort"
}
filtered_reads {
threshold = params.min_reads
report_tag = "MeetsReadThreshold"
}
kraken_bin {
// Python only
taxonomic_level = "G"
fasta_ext = ".fasta.gz"
}
report_aggregate {
sample_flat_suffix = ".flat_sample.json"
}
/*
Base fields for an organism for quality control checking
search: The phrase to search for to determine it is a specific organism
average_quality: average quality of bases must be greater than or equal too
min_n50: n50 value to be greater than or equal too
max_n50: n50 value must be less than or equal too
min_nr_contigs: lower bound minimum of conitgs
max_nr_contigs: upper bound for number of contigs
fixed_genome_size = A set genome size to use for naively calculating genome size
min_length: minimum acceptable length
max_length: maximum acceptable genome length
search =
! Need to provide filtering based on original quality score on raw data
! TODO need to determine if this should happen pre-decon
quality_field = FastP.summary.before_filtering.
raw_average_quality =
min_n50 =
max_n50 =
min_nr_contigs =
max_nr_contigs =
fixed_genome_size =
min_length =
max_length =
max_checkm_contamination = 1.0
average_coverage =
TODO add in tag referencing relevant subtyping tool for including results in final summary csv
*/
QCReport {
escherichia {
search = "Escherichia coli"
raw_average_quality = 30
min_n50 = 50000
max_n50 = 6000000
min_nr_contigs = 1
max_nr_contigs = 500
fixed_genome_size = 5000000
min_length = 4500000
max_length = 6000000
max_checkm_contamination = 3.0
min_average_coverage = 40
}
salmonella {
search = "Salmonella"
raw_average_quality = 30
min_n50 = 90000
max_n50 = 6000000
min_nr_contigs = 1
max_nr_contigs = 200
fixed_genome_size = 5000000
min_length = 4400000
max_length = 6000000
max_checkm_contamination = 3.0
min_average_coverage = 40
}
shigella {
search = "Shigella"
raw_average_quality = 30
min_n50 = 18000
max_n50 = 5000000
min_nr_contigs = 1
max_nr_contigs = 500
fixed_genome_size = 5000000
min_length = 4300000
max_length = 5000000
max_checkm_contamination = 3.0
min_average_coverage = 40
}
listeria {
search = "Listeria"
raw_average_quality = 30
min_n50 = 50000
max_n50 = 3200000
min_nr_contigs = 1
max_nr_contigs = 200
fixed_genome_size = 3000000
min_length = 2700000
max_length = 3200000
max_checkm_contamination = 3.0
min_average_coverage = 30
}
campylobacter_jejuni {
search = "Campylobacter jejuni"
raw_average_quality = 30
min_n50 = 100000
max_n50 = 2000000
min_nr_contigs = 1
max_nr_contigs = 150
fixed_genome_size = 1800000
min_length = 1400000
max_length = 2000000
max_checkm_contamination = 3.0
min_average_coverage = 30
}
campylobacter_coli {
search = "Campylobacter coli"
raw_average_quality = 30
min_n50 = 100000
max_n50 = 2000000
min_nr_contigs = 1
max_nr_contigs = 150
fixed_genome_size = 1800000
min_length = 1400000
max_length = 2000000
max_checkm_contamination = 3.0
min_average_coverage = 30
}
vibrio_cholerae {
search = "Vibrio cholerae"
raw_average_quality = 30
min_n50 = 100000
max_n50 = 4300000
min_nr_contigs = 1
max_nr_contigs = 150
fixed_genome_size = 4000000
min_length = 3800000
max_length = 4300000
max_checkm_contamination = 3.0
min_average_coverage = 40
}
// Some of these defaults are made up
klebsiella {
search = "Klebsiella"
raw_average_quality = 30
min_n50 = 100000
max_n50 = 6000000
min_nr_contigs = 1
max_nr_contigs = 500
fixed_genome_size = 6000000
min_length = 4500000
max_length = 6000000
max_checkm_contamination = 3.0
min_average_coverage = 30
}
staphylococcus {
search = "Staphylococcus"
raw_average_quality = 30
min_n50 = 100000
max_n50 = 3500000
min_nr_contigs = 1
max_nr_contigs = 550
fixed_genome_size = 3500000
min_length = 2000000
max_length = 3500000
max_checkm_contamination = 3.0
min_average_coverage = 30
}
fallthrough {
search = "No organism specific QC data available."
raw_average_quality = 30
min_n50 = null
max_n50 = null
min_nr_contigs = null
max_nr_contigs = null
fixed_genome_size = null
min_length = null
max_length = null
max_checkm_contamination = 3.0
min_average_coverage = 30
}
}
QCReportFields {
// Configure paths if final report where relevant data is required
raw_average_quality {
path = [params.raw_reads.report_tag, "combined", "qual_mean"]
coerce_type = 'Float'
compare_fields = ['raw_average_quality']
comp_type = "ge"
on = true
low_msg = "Base quality is poor, resequencing is recommended."
}
average_coverage {
//path = ["${params.quast.report_tag}", "0", "Avg. coverage depth"] // uncomment to use QUASTS coverage
//path = ["${params.coverage_calc_fields.auto_cov}"] // uncomment to use quasts base_pairs/genome length for coverage
path = ["${params.coverage_calc_fields.fixed_cov}"]
coerce_type = 'Float'
compare_fields = ['min_average_coverage']
comp_type = 'ge'
on = true
low_msg = "Depth of coverage from assembly is lower than than expected. A top-up run is likely needed."
}
metagenomic {
path = [params.mash_meta.report_tag]
coerce_type = 'Bool'
compare_fields = []
comp_type = "bool"
on = false
}
n50_value {
path = [params.quast.report_tag, "0", "N50"]
coerce_type = 'Integer'
compare_fields = ['min_n50', 'max_n50']
comp_type = "range"
on = true
low_msg = "N50 value is low, this could be due to many reasons involving contamination, poor template quality or insufficient template quantity. Reisolation and reseqeuncing may be needed."
high_msg = "N50 value is high, this is likely a good thing if you have fewer contigs than expected."
}
nr_contigs {
path = [params.quast.report_tag, "0", params.quast.contigs_field]
coerce_type = 'Integer'
compare_fields = ['min_nr_contigs', 'max_nr_contigs']
comp_type = "range"
on = true
low_msg = "Fewer contigs than expected, if your genome length is of an expected size and you have a high N50 you likely just have a high quality assembly."
high_msg = "More contigs are present than expected, if your N50 is low and your genome length is shorter than expected you likely need to potentially need to reisolate and resequence/top-up your sample."
}
length {
path = [params.quast.report_tag, "0", "Total length"]
coerce_type = 'Integer'
compare_fields = ['min_length', 'max_length']
comp_type = "range"
on = true
low_msg = "Genome length lower than expected, you may need to resequence the sample."
high_msg = "Genome length is higher than expected, contmination is potentially present."
}
checkm_contamination {
path = [params.checkm.report_tag, "0", "Contamination"]
coerce_type = 'Float'
compare_fields = ['max_checkm_contamination']
comp_type = "le"
on = true
high_msg = "Potential contamination is present in your sample. You may need to reisolate and resequence your sample."
}
}
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load mk-kondo/mikrokondo custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/mikrokondo.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/mikrokondo profiles: ${params.custom_config_base}/pipeline/mikrokondo.config")
// }
profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
}
docker {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
conda.enabled = false
docker.enabled = false