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nextflow_github_test.config
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nextflow_github_test.config
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params {
//Specie parameters
id = "github"
taxon_taxid = "50000"
related_genome = "GCA_002816235.1" // optional, will be used to generate the Jupiter plot
string_telomere = "TTAGGG"
pipeline_version = "V2"
//Optional (if not indicated, autolineage for busco)
// lineage = ""
// lineage2 = "vertebrata_odb10"
// lineage3 = "metazoa_odb10"
// lineage4 = "eukaryota_odb10"
//Data input
raw_data_path = "https://github.com/bcgsc/Canadian_Biogenome_Project/raw/V2/example_input"
//PacBio input
pacbio_input_type = "ccs" // 'hifi' or 'ccs' or 'clr' - HiFi mode: skips filtering
bam_cell1 = "${raw_data_path}/subset_covid_hifi.bam"
// bam_cell2 = "${raw_data_path}/pacbio/"
// bam_cell3 = "${raw_data_path}/pacbio/"
// bam_cell4 = "${raw_data_path}/pacbio/"
//HiC Illumina input
hic_read1 = "${raw_data_path}/test_1.fastq.gz"
hic_read2 = "${raw_data_path}/test_2.fastq.gz"
Illumina_prefix = "test"
//ONT input
// ont_fastq_1 = "${raw_data_path}/nanopore/"
//Illumina short reads input
// illumina_SR_read1 = "${raw_data_path}/SR/"
// illumina_SR_read2 = "${raw_data_path}/SR/"
//Pre-processing
//PacBio reads obtained from SickKids are CCS, not Hifi : It includes HiFi reads but also reads of lower quality.
// This threshold allow to remove reads of lower quality (equivalent to --min-rq in ccs software).
// If 'pacbio_rq'=0.99 --> output bam will contain HiFi Reads with predicted accuracy ≥Q20 (HiFi reads only, Probability of incorrect base call : 1 in 100), equivalent of using extracthifi software
// If 'pacbio_rq'=0.9 --> Phred Quality Score =10, Probability of incorrect base call : 1 in 10
// If 'pacbio_rq'=0.999 --> Phred Quality Score =30, Probability of incorrect base call : 1 in 1000
// For CLR, set 'pacbio_rq'=0.1 to keep all the CLR reads. Canu will deal with them
pacbio_rq = "0.9"
//Method
assembly_method = "hifiasm" // 'hifiasm' or 'canu' of 'flye' or 'verkko'
assembly_secondary_mode = "pacbio" // Depends on the assembly method selected, details in the following lines :
hap2 = "no" // With hifiasm, it is possible to process hap2
// With hifiasm : 'pacbio' (uses pacbio data only), 'pacbio+hic' (--h1 //--h2 : include Hi-C integration, requires Hi-C reads, VGP says that the output requires additional manual curation), 'pacbio+ont' (--ul : Ultra-long ONT integration), 'pacbio+ont+hic'
// With canu : 'hicanu' (-pacbio-hifi : uses HiFi data only), 'ont' (-nanopore : uses nanopore data only), 'clr' (-pacbio : for clr reads (lower quality than hifi))
// With flye : 'hifi' (--pacbio-hifi mode), 'ont' (--nano-raw mode), 'pacbio+ont', 'clr' (--pacbio-raw)
// With verkko : 'pacbio' (--hifi: uses HiFi data only), 'ont' (--nano : uses nanopore data only), 'pacbio+ont' (--hifi --nano)
polishing_method = "none" // 'pilon' or 'none'
purging_method = "purge_dups" // "purge_dups" or "no"
scaffolding_method = "yahs" // 'yahs' or 'salsa'
//Optional steps
mitohifi = "no" // 'yes' or 'no' - Geneerate the mitochondrial assembly
execute_kraken = "no" // 'yes' or 'no' - Assigning taxonomic labels to short DNA sequences
fcs = "no" // 'yes' or 'no' - Foreign contamination screening
methylation_calling = "no" // 'yes' or 'no'
juicer = "no" // 'yes' or 'no' - HiC contact map
genome_comparison = "no" // 'yes' or 'no' - Jupiter plots using circos
blobtools = "no" // 'yes' or 'no' - Overview of data quality
pretext = "no" // 'yes' or 'no' - HiC contact map
run_busco = "no" // 'yes' or 'no'
busco_extend = "limited" // 'every_step' or 'limited'
manual_curation = "none" // 'yes' or 'no' - This parameter doesn't change the pipeline, it is only used to track which assemblies have been manually curated
//If scaffolding_method == 'salsa'
restriction_site = "^GATC,G^ANTC,C^TNAG,T^TAA"
ligation_site = "GATCGATC,GANTGATC,GANTANTC,GATCANTC"
bin_size = "1000000"
//Path - Do not modify
scratch_dir = "$baseDir"
outdir = "${scratch_dir}/${id}/${pipeline_version}/"
busco_lineages_path = "${scratch_dir}/busco_downloads/"
kraken_db = "${scratch_dir}/kraken-db/"
singularity_cache = "${scratch_dir}/singularity/"
fcs_gx_database = "${scratch_dir}/fcs_gx/gxdb/all"
blobtoolkit_path = "${scratch_dir}/blobtoolkit"
modules_path = "${scratch_dir}/pipeline/modules/"
JUICER_JAR = "${singularity_cache}/juicer_tools_1.22.01.jar"
Blobtoolkit_db = "<PATH>/BlobtoolkitDatabase/"
email_adress = "<email>"
}
process {
cache = 'lenient'
executor= "local" // "local" or "slurm"
withLabel:'process_high' {
cpus = 2
memory = '6 GB'
}
withLabel:'process_medium' {
cpus = 2
memory = '6 GB'
}
withLabel:'process_low' {
cpus = 2
memory = '6 GB'
}
withName: 'GOAT_TAXONSEARCH' {
ext.args = "-P -k -G"
}
//Pre-processing
withName: 'BAMTOOLS_FILTER_PACBIO' {
ext.args = [
params.pacbio_rq ? "-tag 'rq':'>=${params.pacbio_rq}'" : '',
].join(' ')
}
//Needed to run the blobtools_pipeline script
withName: 'BAM2FASTX' {
publishDir = [
path: { "${params.outdir}/preprocessing/bam2fastx" },
mode : 'copy',
pattern : "*.fastq.gz"
]
}
withName: 'PREPROCESS_MERGED' {
ext.args_bamtools_filter = [
params.pacbio_rq ? "-tag 'rq':'>=${params.pacbio_rq}'" : '',
].join(' ')
publishDir = [
path: { "${params.outdir}/preprocessing/bam2fastx" },
mode : 'copy',
pattern : "*.fastq.gz"
]
}
withName: 'CUTADAPT' {
ext.args = '--anywhere ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT --anywhere ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT --error-rate 0.1 --overlap 35 --times 3 --revcomp --discard-trimmed'
}
//QC Input data
withName: 'LONGQC_PACBIO' {
ext.args = '-x pb-sequel'
publishDir = [
path: { "${params.outdir}/QC/input_data/LongQC_PacBio" },
mode : 'copy'
]
}
withName: 'LONGQC_ONT' {
ext.args = '-x ont-rapid'
publishDir = [
path: { "${params.outdir}/QC/input_data/LongQC_ONT" },
mode : 'copy'
]
}
withName: 'MERYL_COUNT|MERYL_UNIONSUM|MERYL_HISTOGRAM' {
ext.args = 'k=21'
}
withName: 'GENOMESCOPE2' {
ext.args = '-k 21'
publishDir = [
path: { "${params.outdir}/QC/input_data/genomescope2" },
mode : 'copy',
pattern : "*.png"
]
}
withName: 'KRAKEN2_KRAKEN2_PACBIO_BAM|KRAKEN2_KRAKEN2_HIC_READS|KRAKEN2_KRAKEN2_SR_READS|KRAKEN2_KRAKEN2_ONT_READS' {
cpus=64
memory = '400 GB'
ext.args = '--memory-mapping --quick'
}
//Assembly
//HifiASM
withName: 'HIFIASM' {
cpus=2
memory = '6 GB'
ext.args = '-l 1'
publishDir = [
path: { "${params.outdir}/assembly/1_contig/hifiasm" },
mode : 'copy',
saveAs: { filename -> "$filename" }
]
}
//CANU
withName: 'CANU' {
publishDir = [
path: { "${params.outdir}/assembly/1_contig/canu" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" }
]
}
//FLYE
withName: 'FLYE|FLYE_PACBIO_ONT' {
memory = '300 GB'
}
withName: 'MINIMAP_ALIGN_FLYE' {
ext.args = '-xmap-hifi'
}
withName: 'RACON' {
ext.args = '-m 8 -x -6 -g -8 -w 500'
}
withName: 'LONGSTITCH' {
ext.args = 'z=100'
publishDir = [
path: { "${params.outdir}/assembly/1_contig/flye" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" }
]
}
//VERKKO
withName: 'VERKKO' {
publishDir = [
path: { "${params.outdir}/assembly/1_contig/verkko" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" }
]
}
//MitoHifi
withName: 'MITOHIFI' {
ext.args = '-p 40 -o 2'
publishDir = [
path: { "${params.outdir}/assembly/mitohifi" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" }
]
}
//PILON
////Assembly cleaning
withName: 'FCS_FCSADAPTOR_hap1|FCS_FCSADAPTOR_ALT' {
ext.args = '--euk'
publishDir = [
path: { "${params.outdir}/assembly/2_FCS/fcs_adaptor_cleaned/" },
mode : 'copy',
saveAs: { filename -> "$filename" },
]
}
withName: 'FCS_FCSGX_hap1|FCS_FCSGX_ALT' {
memory = '600 GB'
cpus=42
publishDir = [
path: { "${params.outdir}/assembly/2_FCS/fcs_gx_cleaned/" },
mode : 'copy',
saveAs: { filename -> "$filename" },
]
}
withName: 'FCS_FCSGX_CLEAN_hap1|FCS_FCSGX_CLEAN_ALT' {
publishDir = [
path: { "${params.outdir}/assembly/2_FCS/fcs_gx_cleaned/" },
mode : 'copy',
saveAs: { filename -> "$filename" },
]
}
//PurgeDups
withName: 'PURGEDUPS_CALCUTS_hap1|PURGEDUPS_CALCUTS_ALT' {
ext.args = '-d 1 -u 63'
}
withName: 'MINIMAP2_ALIGN_TO_CONTIG_hap1|MINIMAP2_ALIGN_TO_CONTIG_ALT' {
ext.args = '-x asm5'
}
withName: 'MINIMAP2_ALIGN_TO_SELF_hap1|MINIMAP2_ALIGN_TO_SELF_ALT' {
ext.args = '-DP -k19 -w 19 -m200'
}
withName: 'PURGEDUPS_GETSEQS_hap1|SAMTOOLS_FAIDX1|PURGEDUPS_GETSEQS_ALT|SAMTOOLS_FAIDX1_ALT' {
publishDir = [
path: { "${params.outdir}/assembly/3_purged/purge_dups" },
mode : 'copy'
]
}
//HIC scaffolding
//SALSA2
withName: 'SALSA2' {
ext.args = '-o scaffolds -m CLEAN -e GATC,GANTC,CTNAG,TTAA'
publishDir = [
path: { "${params.outdir}/assembly/4_scaffold/salsa2" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" }
]
}
//YAHS
withName: 'CHROMAP_CHROMAP_hap1|CHROMAP_CHROMAP_ALT' {
ext.args = '--preset hic --remove-pcr-duplicates --SAM'
}
withName: 'YAHS_ALT' {
ext.args = '-l 10 --no-contig-ec -e GATC,GANTC,CTNAG,TTAA'
publishDir = [
path: { "${params.outdir}/assembly/4_scaffold/yahs" },
mode : 'copy',
saveAs: { filename -> "$filename" },
pattern : "*.fa"
]
}
withName: 'YAHS_hap1' {
ext.args = '-l 10 --no-contig-ec -e GATC,GANTC,CTNAG,TTAA'
publishDir = [
path: { "${params.outdir}/manualcuration/" },
mode : 'copy',
]
publishDir = [
path: { "${params.outdir}/assembly/4_scaffold/yahs" },
mode : 'copy',
saveAs: { filename -> "$filename" },
pattern : "*.fa"
]
}
//Assembly QC
//CONTACT Maps
withName: 'SALSA2_JUICER|YAHS_JUICER' {
ext.args = '-a'
publishDir = [
path: { "${params.outdir}/QC/juicer/scaffold/" },
mode : 'copy'
]
}
withName: 'JUICER' {
ext.args = '-S postproc'
publishDir = [
path: { "${params.outdir}/QC/juicer/scaffold/" },
mode : 'copy'
]
}
withName: 'PRETEXTMAP' {
publishDir = [
path: { "${params.outdir}/QC/pretext/pretext/scaffold/" },
mode : 'copy'
]
}
withName: 'PRETEXTGRAPH_TELO_COV|PRETEXTGRAPH_TELO' {
publishDir = [
path: { "${params.outdir}/manualcuration/" },
mode : 'copy',
]
publishDir = [
path: { "${params.outdir}/QC/pretext/pretext/scaffold/" },
mode : 'copy'
]
}
withName: 'PRETEXTSNAPSHOT' {
ext.args = '--sequences "=full, =all"'
cpus=4
memory = '100 GB'
publishDir = [
path: { "${params.outdir}/QC/pretext/pretext/scaffold/" },
mode : 'copy'
]
}
//Assembly continuity
//MERQURY
withName: 'MERQURY_ASS|MERQURY_ASS_DOUBLE' {
publishDir = [
path: { "${params.outdir}/QC/merqury/contig/" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" }
]
}
withName: 'MERQURY_PURGED|MERQURY_PURGED_DOUBLE' {
publishDir = [
path: { "${params.outdir}/QC/merqury/purged" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" }
]
}
withName: 'MERQURY_SCAFF|MERQURY_SCAFF_DOUBLE' {
publishDir = [
path: { "${params.outdir}/QC/merqury/scaffold" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" }
]
}
withName: 'QUAST_ASS|QUAST_ASS_DOUBLE' {
publishDir = [
path: { "${params.outdir}/QC/quast/contig/" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" },
pattern : "report.tsv"
]
}
withName: 'QUAST_PILON' {
publishDir = [
path: { "${params.outdir}/QC/quast/pilon/" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" },
pattern : "report.tsv"
]
}
withName: 'QUAST_CLEAN|QUAST_CLEAN_DOUBLE' {
publishDir = [
path: { "${params.outdir}/QC/quast/FCS/" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" },
pattern : "report.tsv"
]
}
withName: 'QUAST_PURGED|QUAST_PURGED_DOUBLE' {
publishDir = [
path: { "${params.outdir}/QC/quast/purged/" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" },
pattern : "report.tsv"
]
}
withName: 'QUAST_SCAFF|QUAST_SCAFF_DOUBLE' {
publishDir = [
path: { "${params.outdir}/QC/quast/scaffold/" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" },
pattern : "report.tsv"
]
}
// Completeness
withName: 'BUSCO_lin1_PRIM' {
memory = '700 GB'
cpus=32
ext.args = '--mode genome'
publishDir = [
path: { "${params.outdir}/QC/busco/contig_hap1_lin1" },
mode : 'copy',
pattern : "short_summary.*.txt"
]
publishDir = [
path: { "${params.outdir}/QC/busco/contig_hap1_lin1" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" },
pattern : "*full_table.tsv"
]
}
withName: 'BUSCO_lin1_cleaned' {
memory = '700 GB'
cpus=32
ext.args = '--mode genome'
publishDir = [
path: { "${params.outdir}/QC/busco/FCS_hap1_lin1" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" },
pattern : "*full_table.tsv"
]
publishDir = [
path: { "${params.outdir}/QC/busco/FCS_hap1_lin1" },
mode : 'copy',
pattern : "short_summary.*.txt"
]
}
withName: 'BUSCO_lin1_purged' {
memory = '700 GB'
cpus=32
ext.args = '--mode genome'
publishDir = [
path: { "${params.outdir}/QC/busco/purged_hap1_lin1" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" },
pattern : "short_summary.*.txt"
]
publishDir = [
path: { "${params.outdir}/QC/busco/purged_hap1_lin1" },
mode : 'copy',
pattern : "short_summary.*.txt"
]
}
withName: 'BUSCO_lin1_SCAFF' {
memory = '700 GB'
cpus=32
ext.args = '--mode genome'
publishDir = [
path: { "${params.outdir}/QC/busco/scaffold_hap1_lin1" },
mode : 'copy',
pattern : "short_summary.*.txt"
]
publishDir = [
path: { "${params.outdir}/QC/busco/scaffold_hap1_lin1" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" },
pattern : "*full_table.tsv"
]
}
withName: 'BUSCO_lin2' {
memory = '700 GB'
cpus=32
ext.args = '--mode genome'
publishDir = [
path: { "${params.outdir}/QC/busco/hap1_lin2" },
mode : 'copy',
pattern : "short_summary.*.txt"
]
publishDir = [
path: { "${params.outdir}/QC/busco/hap1_lin2" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" },
pattern : "*full_table.tsv"
]
}
withName: 'BUSCO_lin3' {
memory = '700 GB'
cpus=32
ext.args = '--mode genome'
publishDir = [
path: { "${params.outdir}/QC/busco/hap1_lin3" },
mode : 'copy',
pattern : "short_summary.*.txt"
]
publishDir = [
path: { "${params.outdir}/QC/busco/hap1_lin3" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" },
pattern : "*full_table.tsv"
]
}
withName: 'BUSCO_lin4' {
memory = '700 GB'
cpus=32
ext.args = '--mode genome'
publishDir = [
path: { "${params.outdir}/QC/busco/hap1_lin4" },
mode : 'copy',
pattern : "short_summary.*.txt"
]
publishDir = [
path: { "${params.outdir}/QC/busco/hap1_lin4" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" },
pattern : "*full_table.tsv"
]
}
withName: 'BUSCO_ALT' {
memory = '700 GB'
cpus=32
ext.args = '--mode genome'
publishDir = [
path: { "${params.outdir}/QC/busco/hap2_lin1" },
mode : 'copy',
pattern : "short_summary.*.txt"
]
publishDir = [
path: { "${params.outdir}/QC/busco/hap2_lin1" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" },
pattern : "*full_table.tsv"
]
}
//Methylation
withName: 'JASMINE|PBMM2|SAMTOOLS_INDEX_PBMM2' {
publishDir = [
path: { "${params.outdir}/methylation/" },
mode : 'copy',
]
}
//BLOBTOOLSKIT
withName: 'GZIP|BLOBTOOLS_CONFIG|BLOBTOOLS_PIPELINE|BLOBTOOLS_CREATE|BLOBTOOLS_ADD|BLOBTOOLS_VIEW' {
publishDir = [
path: { "${params.outdir}/QC/blobtools/" },
mode : 'copy',
]
}
withName: 'RAPIDCURATION_SPLIT' {
publishDir = [
path: { "${params.outdir}/manualcuration/" },
mode : 'copy',
]
}
// Genome COmparison
withName: 'NCBIGENOMEDOWNLOAD' {
ext.args = [
params.related_genome ? "-s genbank -A ${params.related_genome} --formats fasta all" : ''
].join(' ')
}
withName: 'MASHMAP' {
ext.args = '-f one-to-one --pi 95 -s 100000'
publishDir = [
path: { "${params.outdir}/QC/mashmap/scaffold/" },
mode : 'copy',
]
}
withName: 'JUPITER' {
ext.args = 'ng=90'
publishDir = [
path: { "${params.outdir}/QC/jupiter/scaffold/" },
mode : 'copy',
]
}
withName: 'BEDTOOLS_GENOMECOV' {
ext.args = '-bga'
}
//MultiQC
withName: 'MULTIQC' {
ext.args = '--fullnames --force'
publishDir = [
path: { "${params.outdir}/QC/multiqc" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" },
pattern : "*_report.html"
]
}
//Overview
withName: 'OVERVIEW_GENERATION_SAMPLE' {
publishDir = [
path: { "${params.outdir}/QC/overview" },
mode : 'copy',
saveAs: { filename -> "${params.id}_$filename" },
]
}
withName: 'CUSTOM_DUMPSOFTWAREVERSIONS' {
publishDir = [
path: { "${params.outdir}/QC/versions/" },
mode : 'copy',
]
}
}
conda{
enabled = true
createOptions = '--channel conda-forge'
}
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
mamba {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
gitpod {
executor.name = 'local'
executor.cpus = 16
executor.memory = 60.GB
}
}