Earth Biogenome Project - Pilot Workflow

The primary workflow for the Earth Biogenome Project Pilot at NBIS.

Workflow overview

General aim:

flowchart LR
    hifi[/ HiFi reads /] --> data_inspection
    ont[/ ONT reads /] -->  data_inspection
    hic[/ Hi-C reads /] --> data_inspection
    data_inspection[[ Data inspection ]] --> preprocessing
    preprocessing[[ Preprocessing ]] --> assemble
    assemble[[ Assemble ]] --> validation
    validation[[ Assembly validation ]] --> curation
    curation[[ Assembly curation ]] --> validation

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Current implementation:

flowchart TD
    input[/ Input file/] --> hifi
    input --> hic
    input --> taxquery[[ ENA taxonomic query ]]
    taxquery --> goat_taxon[[ GOAT taxon search ]]
    goat_taxon --> busco
    goat_taxon --> dtol[[ DToL lookup ]]
    hifi --> samtools_fa[[ Samtools fasta ]]
    samtools_fa --> fastk_hifi
    hifi[/ HiFi reads /] --> fastk_hifi[[ FastK - HiFi ]]
    hifi --> meryl_hifi[[ Meryl - HiFi ]]
    hic[/ Hi-C reads /] --> fastk_hic[[ FastK - Hi-C ]]
    hifi --> meryl_hic[[ Meryl - Hi-C ]]
    hic --> fastqc_hic[[ FastQC - Hi-C ]]
    hic --> seqkit_hic[[ SeqKit Stats - Hi-C ]]
    hifi --> seqkit_hifi[[ SeqKit Stats - HiFi ]]
    assembly[/ Assembly /] --> quast[[ Quast ]]
    fastk_hifi --> histex[[ Histex ]]
    histex --> genescopefk[[ GeneScopeFK ]]
    fastk_hifi --> ploidyplot[[ PloidyPlot ]]
    fastk_hifi --> katgc[[ KatGC ]]
    fastk_hifi --> merquryfk[[ MerquryFK ]]
    assembly --> merquryfk
    meryl_hifi --> merqury[[ Merqury ]]
    assembly --> merqury
    fastk_hifi --> katcomp[[ KatComp ]]
    fastk_hic --> katcomp
    assembly --> busco[[ Busco ]]
    fastk_hifi --> hifiasm[[ HiFiasm ]]
    hifiasm --> assembly
    assembly --> purgedups[[ Purgedups ]]
    input --> mitoref[[ Mitohifi - Find reference ]]
    assembly --> mitohifi[[ Mitohifi ]]
    assembly --> fcsgx[[ FCS GX ]]
    fcs_fetchdb[( FCS fetchdb )] --> fcsgx
    mitoref --> mitohifi
    genescopefk --> quarto[[ Quarto ]]
    goat_taxon --> multiqc[[ MultiQC ]]
    quarto --> multiqc
    dtol --> multiqc
    katgc --> multiqc
    ploidyplot --> multiqc
    busco --> multiqc
    quast --> multiqc

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Usage

nextflow run -params-file <params.yml> \
    [ -c <custom.config> ] \
    [ -profile <profile> ] \
    NBISweden/Earth-Biogenome-Project-pilot

where:

• params.yml is a YAML formatted file containing workflow parameters such as input paths to the assembly specification, and settings for tools within the workflow.

  Example:

  input: 'assembly_spec.yml'
  outdir: results
  fastk: # Optional
    kmer_size: 31 # default 31
  genescopefk: # Optional
    kmer_size: 31 # default 31
  hifiasm: # Optional, default = no extra options: Key (e.g. 'opts01') is used in assembly build name (e.g., 'hifiasm-raw-opts01').
    opts01: "--opts A"
    opts02: "--opts B"
  busco: # Optional, default: retrieved by GOAT_TAXONSEARCH
    lineages: 'auto' # comma separated string of lineages or auto.

  Alternatively parameters can be provided on the command-line using the --parameter notation (e.g., --input <path> ).

• <custom.config> is a Nextflow configuration file which provides additional configuration. This is used to customise settings other than workflow parameters, such as cpus, time, and command-line options to tools.

  Example:

  process {
      withName: 'BUSCO' {  // Selects the process to apply settings.
          cpus     = 6     // Overrides cpu settings defined in nextflow.config
          time     = 4.d   // Overrides time settings defined in nextflow.config to 4 days. Use .h for hours, .m for minutes.
          memory   = '20GB'  // Overrides memory settings defined in nextflow.config to 20 GB.
          // ext.args supplies command-line options to the process tool
          // overrides settings found in configs/modules.config
          ext.args = '--long'  // Supplies these as command-line options to Busco
      }
  }

• <profile> is one of the preconfigured execution profiles (<cluster_specific_profile>, singularity, docker, etc: see nextflow.config). Alternatively, you can provide a custom configuration to configure this workflow to your execution environment. See Nextflow Configuration for more details.

Workflow parameter inputs

Mandatory:

• input: A YAML formatted input file. Example assembly_spec.yml (See also test profile input TODO:: Update test profile):

  sample:                          # Required: Meta data
    name: 'Laetiporus sulphureus'  # Required: Species name. Correct spelling is important to look up species information.
    ploidy: 2                      # Optional: Estimated ploidy (default: retrieved by GOAT_TAXONSEARCH)
    genome_size: 2345              # Optional: Estimated genome size (default: retrieved by GOAT_TAXONSEARCH)
    haploid_number: 13             # Optional: Estimated haploid chromosome count (default: retrieved by GOAT_TAXONSEARCH)
    tax_id: 5630                   # Optional: Taxon ID (default: retrieved by ENA_TAXQUERY)
    genetic_code: 1                # Optional: Genetic code (default: retrieved by ENA_TAXQUERY)
    mito_code: 1                   # Optional: Mitochondrial genetic code (default: retrieved by ENA_TAXQUERY)
    domain: Eukaryota              # Optional: (default: retrived by ENA_TAXQUERY)
  assembly:                        # Optional: List of assemblies to curate and validate.
    - assembler: hifiasm           # For each entry, the assembler,
      stage: raw                   # stage of assembly (raw, decontaminated, purged, polished, scaffolded, curated),
      id: uuid                     # unique id,
      pri_fasta: /path/to/primary_asm.fasta # and paths to sequences are required.
      alt_fasta: /path/to/alternate_asm.fasta
      pri_gfa: /path/to/primary_asm.gfa
      alt_gfa: /path/to/alternate_asm.gfa
    - assembler: ipa
      stage: raw
      id: uuid
      pri_fasta: /path/to/primary_asm.fasta
      alt_fasta: /path/to/alternate_asm.fasta
  hic:                             # Optional: List of hi-c reads to QC and use for scaffolding
    - read1: '/path/to/raw/data/hic/LS_HIC_R001_1.fastq.gz'
      read2: '/path/to/raw/data/hic/LS_HIC_R001_2.fastq.gz'
  hifi:                            # Required: List of hifi-reads to QC and use for assembly/validation
    - reads: '/path/to/raw/data/hifi/LS_HIFI_R001.bam'
  rnaseq:                          # Optional: List of Rna-seq reads to use for validation
    - read1: '/path/to/raw/data/rnaseq/LS_RNASEQ_R001_1.fastq.gz'
      read2: '/path/to/raw/data/rnaseq/LS_RNASEQ_R001_2.fastq.gz'
  isoseq:                          # Optional: List of Isoseq reads to use for validation
    - reads: '/path/to/raw/data/isoseq/LS_ISOSEQ_R001.bam'

Optional:

• outdir: The publishing path for results (default: results).

• publish_mode: (values: 'symlink' (default), 'copy') The file publishing method from the intermediate results folders (see Table of publish modes).

• steps: The workflow steps to execute (default is all steps). Choose from:

  • inspect: 01 - Read inspection
  • preprocess: 02 - Read preprocessing
  • assemble: 03 - Assembly
  • screen: 04 - Contamination screening
  • purge: 05 - Duplicate purging
  • polish: 06 - Error polishing (TODO: In development)
  • scaffold: 07 - Scaffolding
  • curate: 08 - Rapid curation
  • alignRNA: 09 - Align RNAseq data

Software specific:

Tool specific settings are provided by supplying values to specific keys or supplying an array of settings under a tool name. The input to -params-file would look like this:

input: assembly.yml
outdir: results
fastk:
  kmer_size: 31
genescopefk:
  kmer_size: 31
hifiasm:
  opts01: "--opts A"
  opts02: "--opts B"
busco:
  lineages: 'auto'

• multiqc_config: Path to MultiQC configuration file (default: configs/multiqc_conf.yaml).

Workflow outputs

All results are published to the path assigned to the workflow parameter outdir.

Expand for example results directory structure

results
├── 01_read_inspection
│   ├── dtol_search
│   │   └── 7227_tol_info.json
│   ├── fastk
│   │   ├── Drosophila_melanogaster_dmel_2Mb.fasta_hifi_fk.hist
│   │   ├── Drosophila_melanogaster_dmel_2Mb.fasta_hifi_fk.ktab
│   │   ├── Drosophila_melanogaster_dmel_2Mb_p1_1.fastp.fastq_hic_fk.hist
│   │   ├── Drosophila_melanogaster_dmel_2Mb_p1_1.fastp.fastq_hic_fk.ktab
│   │   ├── Drosophila_melanogaster_dmel_2Mb_p2_1.fastp.fastq_hic_fk.hist
│   │   ├── Drosophila_melanogaster_dmel_2Mb_p2_1.fastp.fastq_hic_fk.ktab
│   │   ├── Drosophila_melanogaster_merged_hic.hist
│   │   └── Drosophila_melanogaster_merged_hic.ktab
│   ├── fastqc_hic
│   │   ├── dmel_2Mb_p1_R1_1_fastqc.html
│   │   ├── dmel_2Mb_p1_R1_1_fastqc.zip
│   │   ├── dmel_2Mb_p1_R1_2_fastqc.html
│   │   ├── dmel_2Mb_p1_R1_2_fastqc.zip
│   │   ├── dmel_2Mb_p2_R1_1_fastqc.html
│   │   ├── dmel_2Mb_p2_R1_1_fastqc.zip
│   │   ├── dmel_2Mb_p2_R1_2_fastqc.html
│   │   └── dmel_2Mb_p2_R1_2_fastqc.zip
│   ├── genescopefk
│   │   ├── Drosophila_melanogaster_linear_plot.png
│   │   ├── Drosophila_melanogaster_log_plot.png
│   │   ├── Drosophila_melanogaster_model.txt
│   │   ├── Drosophila_melanogaster_summary.txt
│   │   ├── Drosophila_melanogaster_transformed_linear_plot.png
│   │   └── Drosophila_melanogaster_transformed_log_plot.png
│   ├── kat_comp
│   │   ├── Drosophila_melanogaster_katcomp.fi.png
│   │   ├── Drosophila_melanogaster_katcomp.ln.png
│   │   └── Drosophila_melanogaster_katcomp.st.png
│   ├── katgc
│   │   ├── Drosophila_melanogaster_katgc.fi.png
│   │   ├── Drosophila_melanogaster_katgc.ln.png
│   │   └── Drosophila_melanogaster_katgc.st.png
│   ├── ploidyplot
│   │   ├── Drosophila_melanogaster_ploidyplot.fi.png
│   │   ├── Drosophila_melanogaster_ploidyplot.ln.png
│   │   └── Drosophila_melanogaster_ploidyplot.st.png
│   ├── seqkit_hic_stats
│   │   ├── dmel_2Mb_p1_R1_hic.tsv
│   │   └── dmel_2Mb_p2_R1_hic.tsv
│   └── seqkit_hifi_stats
│       └── dmel_2Mb_hifi.tsv
├── 02_read_preprocessing
│   └── hi-c_cram
│       ├── dmel_2Mb_p1.cram
│       ├── dmel_2Mb_p1.cram.crai
│       ├── dmel_2Mb_p2.cram
│       └── dmel_2Mb_p2.cram.crai
├── 03_assembly
│   ├── busco
│   │   └── hifiasm-raw-default
│   │       ├── hifiasm-raw-default-bacteria_odb10-busco.batch_summary.txt
│   │       ├── short_summary.specific.bacteria_odb10.hifiasm-raw-default.bp.p_ctg.fasta.json
│   │       └── short_summary.specific.bacteria_odb10.hifiasm-raw-default.bp.p_ctg.fasta.txt
│   ├── gfastats
│   │   └── hifiasm-raw-default
│   │       └── hifiasm-raw-default.bp.p_ctg.fasta.assembly_summary
│   ├── hifiasm-raw-default
│   │   ├── hifiasm-raw-default.bp.hap1.p_ctg.gfa
│   │   ├── hifiasm-raw-default.bp.hap2.p_ctg.gfa
│   │   ├── hifiasm-raw-default.bp.p_ctg.fasta.gz
│   │   ├── hifiasm-raw-default.bp.p_ctg.gfa
│   │   ├── hifiasm-raw-default.bp.p_utg.gfa
│   │   ├── hifiasm-raw-default.bp.r_utg.gfa
│   │   ├── hifiasm-raw-default.ec.bin
│   │   ├── hifiasm-raw-default.ovlp.reverse.bin
│   │   ├── hifiasm-raw-default.ovlp.source.bin
│   │   └── hifiasm-raw-default.stderr.log
│   ├── merqury
│   │   └── hifiasm-raw-default
│   │       ├── Drosophila_melanogaster_hifi.unionsumdb.hist.ploidy
│   │       ├── hifiasm-raw-default.bp.p_ctg_only.bed
│   │       ├── hifiasm-raw-default.bp.p_ctg_only.wig
│   │       ├── hifiasm-raw-default_merqury.completeness.stats
│   │       ├── hifiasm-raw-default_merqury.dist_only.hist
│   │       ├── hifiasm-raw-default_merqury.hifiasm-raw-default.bp.p_ctg.qv
│   │       ├── hifiasm-raw-default_merqury.hifiasm-raw-default.bp.p_ctg.spectra-cn.fl.png
│   │       ├── hifiasm-raw-default_merqury.hifiasm-raw-default.bp.p_ctg.spectra-cn.hist
│   │       ├── hifiasm-raw-default_merqury.hifiasm-raw-default.bp.p_ctg.spectra-cn.ln.png
│   │       ├── hifiasm-raw-default_merqury.hifiasm-raw-default.bp.p_ctg.spectra-cn.st.png
│   │       ├── hifiasm-raw-default_merqury.qv
│   │       ├── hifiasm-raw-default_merqury.spectra-asm.fl.png
│   │       ├── hifiasm-raw-default_merqury.spectra-asm.hist
│   │       ├── hifiasm-raw-default_merqury.spectra-asm.ln.png
│   │       └── hifiasm-raw-default_merqury.spectra-asm.st.png
│   └── merquryfk
│       └── hifiasm-raw-default
│           ├── hifiasm-raw-default_merquryfk.cni.gz
│           ├── hifiasm-raw-default_merquryfk.completeness.stats
│           ├── hifiasm-raw-default_merquryfk.false_duplications.tsv
│           ├── hifiasm-raw-default_merquryfk.hifiasm-raw-default.bp.p_ctg.qv
│           ├── hifiasm-raw-default_merquryfk.hifiasm-raw-default.bp.p_ctg.spectra-cn.fl.png
│           ├── hifiasm-raw-default_merquryfk.hifiasm-raw-default.bp.p_ctg.spectra-cn.ln.png
│           ├── hifiasm-raw-default_merquryfk.hifiasm-raw-default.bp.p_ctg.spectra-cn.st.png
│           ├── hifiasm-raw-default_merquryfk.hifiasm-raw-default.bp.p_ctg_only.bed
│           ├── hifiasm-raw-default_merquryfk.qv
│           ├── hifiasm-raw-default_merquryfk.spectra-asm.fl.png
│           ├── hifiasm-raw-default_merquryfk.spectra-asm.ln.png
│           └── hifiasm-raw-default_merquryfk.spectra-asm.st.png
├── 05_duplicate_purging
│   ├── busco
│   │   └── hifiasm-purged-default
│   │       ├── hifiasm-purged-default-bacteria_odb10-busco.batch_summary.txt
│   │       ├── short_summary.specific.bacteria_odb10.Drosophila_melanogaster_hifiasm-purged-default_hap0.purged_fold.fasta.json
│   │       └── short_summary.specific.bacteria_odb10.Drosophila_melanogaster_hifiasm-purged-default_hap0.purged_fold.fasta.txt
│   ├── gfastats
│   │   └── hifiasm-purged-default
│   │       └── Drosophila_melanogaster_hifiasm-purged-default_hap0.purged_fold.assembly_summary
│   ├── merqury
│   │   └── hifiasm-purged-default
│   │       ├── Drosophila_melanogaster_hifi.unionsumdb.hist.ploidy
│   │       ├── Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold_only.bed
│   │       ├── Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold_only.wig
│   │       ├── Drosophila_melanogaster_hifiasm-purged-default_hap0.purged_fold_only.bed
│   │       ├── Drosophila_melanogaster_hifiasm-purged-default_hap0.purged_fold_only.wig
│   │       ├── hifiasm-purged-default_merqury.Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold.qv
│   │       ├── hifiasm-purged-default_merqury.Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold.spectra-cn.fl.png
│   │       ├── hifiasm-purged-default_merqury.Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold.spectra-cn.hist
│   │       ├── hifiasm-purged-default_merqury.Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold.spectra-cn.ln.png
│   │       ├── hifiasm-purged-default_merqury.Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold.spectra-cn.st.png
│   │       ├── hifiasm-purged-default_merqury.Drosophila_melanogaster_hifiasm-purged-default_hap0.purged_fold.qv
│   │       ├── hifiasm-purged-default_merqury.Drosophila_melanogaster_hifiasm-purged-default_hap0.purged_fold.spectra-cn.fl.png
│   │       ├── hifiasm-purged-default_merqury.Drosophila_melanogaster_hifiasm-purged-default_hap0.purged_fold.spectra-cn.hist
│   │       ├── hifiasm-purged-default_merqury.Drosophila_melanogaster_hifiasm-purged-default_hap0.purged_fold.spectra-cn.ln.png
│   │       ├── hifiasm-purged-default_merqury.Drosophila_melanogaster_hifiasm-purged-default_hap0.purged_fold.spectra-cn.st.png
│   │       ├── hifiasm-purged-default_merqury.completeness.stats
│   │       ├── hifiasm-purged-default_merqury.dist_only.hist
│   │       ├── hifiasm-purged-default_merqury.qv
│   │       ├── hifiasm-purged-default_merqury.spectra-asm.fl.png
│   │       ├── hifiasm-purged-default_merqury.spectra-asm.hist
│   │       ├── hifiasm-purged-default_merqury.spectra-asm.ln.png
│   │       ├── hifiasm-purged-default_merqury.spectra-asm.st.png
│   │       ├── hifiasm-purged-default_merqury.spectra-cn.fl.png
│   │       ├── hifiasm-purged-default_merqury.spectra-cn.hist
│   │       ├── hifiasm-purged-default_merqury.spectra-cn.ln.png
│   │       └── hifiasm-purged-default_merqury.spectra-cn.st.png
│   ├── merquryfk
│   │   └── hifiasm-purged-default
│   │       ├── hifiasm-purged-default_merquryfk.Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold.qv
│   │       ├── hifiasm-purged-default_merquryfk.Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold.spectra-cn.fl.png
│   │       ├── hifiasm-purged-default_merquryfk.Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold.spectra-cn.ln.png
│   │       ├── hifiasm-purged-default_merquryfk.Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold.spectra-cn.st.png
│   │       ├── hifiasm-purged-default_merquryfk.Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold_only.bed
│   │       ├── hifiasm-purged-default_merquryfk.Drosophila_melanogaster_hifiasm-purged-default_hap0.purged_fold.qv
│   │       ├── hifiasm-purged-default_merquryfk.Drosophila_melanogaster_hifiasm-purged-default_hap0.purged_fold.spectra-cn.fl.png
│   │       ├── hifiasm-purged-default_merquryfk.Drosophila_melanogaster_hifiasm-purged-default_hap0.purged_fold.spectra-cn.ln.png
│   │       ├── hifiasm-purged-default_merquryfk.Drosophila_melanogaster_hifiasm-purged-default_hap0.purged_fold.spectra-cn.st.png
│   │       ├── hifiasm-purged-default_merquryfk.Drosophila_melanogaster_hifiasm-purged-default_hap0.purged_fold_only.bed
│   │       ├── hifiasm-purged-default_merquryfk.cni.gz
│   │       ├── hifiasm-purged-default_merquryfk.completeness.stats
│   │       ├── hifiasm-purged-default_merquryfk.false_duplications.tsv
│   │       ├── hifiasm-purged-default_merquryfk.qv
│   │       ├── hifiasm-purged-default_merquryfk.spectra-asm.fl.png
│   │       ├── hifiasm-purged-default_merquryfk.spectra-asm.ln.png
│   │       ├── hifiasm-purged-default_merquryfk.spectra-asm.st.png
│   │       ├── hifiasm-purged-default_merquryfk.spectra-cn.fl.png
│   │       ├── hifiasm-purged-default_merquryfk.spectra-cn.ln.png
│   │       └── hifiasm-purged-default_merquryfk.spectra-cn.st.png
│   └── purge_dups
│       ├── Drosophila_melanogaster.PB.base.cov
│       ├── Drosophila_melanogaster.PB.stat
│       ├── Drosophila_melanogaster.calcuts.log
│       ├── Drosophila_melanogaster.cutoffs
│       ├── Drosophila_melanogaster_hifiasm-purged-default_hap0.dups.bed
│       ├── Drosophila_melanogaster_hifiasm-purged-default_hap0.hap.fa
│       ├── Drosophila_melanogaster_hifiasm-purged-default_hap0.merged.fasta.gz
│       ├── Drosophila_melanogaster_hifiasm-purged-default_hap0.purge_dups.log
│       ├── Drosophila_melanogaster_hifiasm-purged-default_hap0.purged.fa
│       ├── Drosophila_melanogaster_hifiasm-purged-default_hap0.split.fasta.gz
│       └── Drosophila_melanogaster_hifiasm-purged-default_purgedups_hist.png
├── 07_scaffolding
│   ├── busco
│   │   └── hifiasm-scaffolded-default
│   │       ├── hifiasm-scaffolded-default-bacteria_odb10-busco.batch_summary.txt
│   │       ├── short_summary.specific.bacteria_odb10.Drosophila_melanogaster_hifiasm-scaffolded-default_scaffolds_final.fa.json
│   │       └── short_summary.specific.bacteria_odb10.Drosophila_melanogaster_hifiasm-scaffolded-default_scaffolds_final.fa.txt
│   ├── gfastats
│   │   └── hifiasm-scaffolded-default
│   │       └── Drosophila_melanogaster_hifiasm-scaffolded-default_scaffolds_final.assembly_summary
│   ├── merqury
│   │   └── hifiasm-scaffolded-default
│   │       ├── Drosophila_melanogaster_hifi.unionsumdb.hist.ploidy
│   │       ├── Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold_only.bed
│   │       ├── Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold_only.wig
│   │       ├── Drosophila_melanogaster_hifiasm-scaffolded-default_scaffolds_final_only.bed
│   │       ├── Drosophila_melanogaster_hifiasm-scaffolded-default_scaffolds_final_only.wig
│   │       ├── hifiasm-scaffolded-default_merqury.Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold.qv
│   │       ├── hifiasm-scaffolded-default_merqury.Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold.spectra-cn.fl.png
│   │       ├── hifiasm-scaffolded-default_merqury.Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold.spectra-cn.hist
│   │       ├── hifiasm-scaffolded-default_merqury.Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold.spectra-cn.ln.png
│   │       ├── hifiasm-scaffolded-default_merqury.Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold.spectra-cn.st.png
│   │       ├── hifiasm-scaffolded-default_merqury.Drosophila_melanogaster_hifiasm-scaffolded-default_scaffolds_final.qv
│   │       ├── hifiasm-scaffolded-default_merqury.Drosophila_melanogaster_hifiasm-scaffolded-default_scaffolds_final.spectra-cn.fl.png
│   │       ├── hifiasm-scaffolded-default_merqury.Drosophila_melanogaster_hifiasm-scaffolded-default_scaffolds_final.spectra-cn.hist
│   │       ├── hifiasm-scaffolded-default_merqury.Drosophila_melanogaster_hifiasm-scaffolded-default_scaffolds_final.spectra-cn.ln.png
│   │       ├── hifiasm-scaffolded-default_merqury.Drosophila_melanogaster_hifiasm-scaffolded-default_scaffolds_final.spectra-cn.st.png
│   │       ├── hifiasm-scaffolded-default_merqury.completeness.stats
│   │       ├── hifiasm-scaffolded-default_merqury.dist_only.hist
│   │       ├── hifiasm-scaffolded-default_merqury.qv
│   │       ├── hifiasm-scaffolded-default_merqury.spectra-asm.fl.png
│   │       ├── hifiasm-scaffolded-default_merqury.spectra-asm.hist
│   │       ├── hifiasm-scaffolded-default_merqury.spectra-asm.ln.png
│   │       ├── hifiasm-scaffolded-default_merqury.spectra-asm.st.png
│   │       ├── hifiasm-scaffolded-default_merqury.spectra-cn.fl.png
│   │       ├── hifiasm-scaffolded-default_merqury.spectra-cn.hist
│   │       ├── hifiasm-scaffolded-default_merqury.spectra-cn.ln.png
│   │       └── hifiasm-scaffolded-default_merqury.spectra-cn.st.png
│   ├── merquryfk
│   │   └── hifiasm-scaffolded-default
│   │       ├── hifiasm-scaffolded-default_merquryfk.Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold.qv
│   │       ├── hifiasm-scaffolded-default_merquryfk.Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold.spectra-cn.fl.png
│   │       ├── hifiasm-scaffolded-default_merquryfk.Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold.spectra-cn.ln.png
│   │       ├── hifiasm-scaffolded-default_merquryfk.Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold.spectra-cn.st.png
│   │       ├── hifiasm-scaffolded-default_merquryfk.Drosophila_melanogaster_hifiasm-purged-default_hap0.hap_fold_only.bed
│   │       ├── hifiasm-scaffolded-default_merquryfk.Drosophila_melanogaster_hifiasm-scaffolded-default_scaffolds_final.qv
│   │       ├── hifiasm-scaffolded-default_merquryfk.Drosophila_melanogaster_hifiasm-scaffolded-default_scaffolds_final.spectra-cn.fl.png
│   │       ├── hifiasm-scaffolded-default_merquryfk.Drosophila_melanogaster_hifiasm-scaffolded-default_scaffolds_final.spectra-cn.ln.png
│   │       ├── hifiasm-scaffolded-default_merquryfk.Drosophila_melanogaster_hifiasm-scaffolded-default_scaffolds_final.spectra-cn.st.png
│   │       ├── hifiasm-scaffolded-default_merquryfk.Drosophila_melanogaster_hifiasm-scaffolded-default_scaffolds_final_only.bed
│   │       ├── hifiasm-scaffolded-default_merquryfk.cni.gz
│   │       ├── hifiasm-scaffolded-default_merquryfk.completeness.stats
│   │       ├── hifiasm-scaffolded-default_merquryfk.false_duplications.tsv
│   │       ├── hifiasm-scaffolded-default_merquryfk.qv
│   │       ├── hifiasm-scaffolded-default_merquryfk.spectra-asm.fl.png
│   │       ├── hifiasm-scaffolded-default_merquryfk.spectra-asm.ln.png
│   │       ├── hifiasm-scaffolded-default_merquryfk.spectra-asm.st.png
│   │       ├── hifiasm-scaffolded-default_merquryfk.spectra-cn.fl.png
│   │       ├── hifiasm-scaffolded-default_merquryfk.spectra-cn.ln.png
│   │       └── hifiasm-scaffolded-default_merquryfk.spectra-cn.st.png
│   ├── pairtools
│   │   └── hifiasm-scaffolded-default
│   │       ├── Drosophila_melanogaster_hifiasm-scaffolded-default_dedup.pairs.stat
│   │       ├── Drosophila_melanogaster_hifiasm-scaffolded-default_dmel_2Mb_p1_1.fastp.pairsam.stat
│   │       └── Drosophila_melanogaster_hifiasm-scaffolded-default_dmel_2Mb_p2_1.fastp.pairsam.stat
│   └── yahs
│       └── hifiasm-scaffolded-default
│           ├── Drosophila_melanogaster_hifiasm-scaffolded-default.bin
│           ├── Drosophila_melanogaster_hifiasm-scaffolded-default_scaffolds_final.agp
│           └── Drosophila_melanogaster_hifiasm-scaffolded-default_scaffolds_final.fa
├── 08_curation
│   ├── higlass
│   │   └── hifiasm-curated-default
│   │       ├── hifiasm-curated-default_gaps.bedgraph.beddb
│   │       ├── hifiasm-curated-default_merged_dupMarked.mcool
│   │       └── hifiasm-curated-default_telomer.bw
│   └── pretext
│       └── hifiasm-curated-default
│           └── hifiasm-curated-default_wTracks.pretext
├── 10_report
│   ├── assembly_report.html
│   ├── assembly_report.md
│   ├── multiqc-summary.html
│   ├── quast
│   │   ├── Drosophila_melanogaster_quast_report
│   │   │   ├── basic_stats
│   │   │   │   ├── Drosophila_melanogaster_hifiasm-purged-default_hap0.purged_fold_GC_content_plot.pdf
│   │   │   │   ├── Drosophila_melanogaster_hifiasm-scaffolded-default_scaffolds_final_GC_content_plot.pdf
│   │   │   │   ├── GC_content_plot.pdf
│   │   │   │   ├── Nx_plot.pdf
│   │   │   │   ├── cumulative_plot.pdf
│   │   │   │   └── hifiasm-raw-default.bp.p_ctg_GC_content_plot.pdf
│   │   │   ├── icarus.html
│   │   │   ├── icarus_viewers
│   │   │   │   └── contig_size_viewer.html
│   │   │   ├── quast.log
│   │   │   ├── report.html
│   │   │   ├── report.pdf
│   │   │   ├── report.tex
│   │   │   ├── report.tsv
│   │   │   ├── report.txt
│   │   │   ├── transposed_report.tex
│   │   │   ├── transposed_report.tsv
│   │   │   └── transposed_report.txt
│   │   └── Drosophila_melanogaster_quast_report.tsv
│   └── versions.yml
└── pipeline_info
    ├── execution_report_2025-10-14_11-58-07.html
    ├── execution_timeline_2025-10-14_11-58-07.html
    ├── execution_trace_2025-10-14_11-58-07.txt
    └── pipeline_dag_2025-10-14_11-58-07.mmd

Examples

• Run the workflow with the default parameters and all steps:

  nextflow run NBISweden/Earth-Biogenome-Project-pilot -params-file params.yml

  where params.yml is a YAML file containing the workflow parameters:

  input: 'assembly_spec.yml'

  and assembly_spec.yml is a YAML file containing the assembly specification

  sample:
    name: 'Laetiporus sulphureus'
  hifi:
    - reads: '/path/to/raw/data/hifi/LS_HIFI_R001.bam'
  hic:
    - read1: '/path/to/raw/data/hic/LS_HIC_R001_1.fastq.gz'
      read2: '/path/to/raw/data/hic/LS_HIC_R001_2.fastq.gz'

• Run purging to curation on an existing assembly:

  nextflow run NBISweden/Earth-Biogenome-Project-pilot -params-file params.yml

  where params.yml is a YAML file containing the workflow parameters:

  input: 'assembly_spec.yml'
  steps: 'purge,scaffold,curate'

  and assembly_spec.yml is a YAML file containing the assembly specification

  sample:
    name: 'Laetiporus sulphureus'
  assembly:
    - assembler: hifiasm
      stage: decontaminated
      id: uuid
      pri_fasta: '/path/to/primary_asm-hifiasm-decontaminated-uuid.fasta'
  hifi:
    - reads: '/path/to/raw/data/hifi/LS_HIFI_R001.bam'
  hic:
    - read1: '/path/to/raw/data/hic/LS_HIC_R001_1.fastq.gz'
      read2: '/path/to/raw/data/hic/LS_HIC_R001_2.fastq.gz'

• Run the workflow to only run assembly evaluation.

  nextflow run NBISweden/Earth-Biogenome-Project-pilot -params-file params.yml

  where params.yml is a YAML file containing the workflow parameters:

  input: 'assembly_spec.yml'
  steps: 'curate'

  and assembly_spec.yml is a YAML file containing the assembly specification

  sample:
    name: 'Laetiporus sulphureus'
  # Assembly to evaluate
  assembly:
    - assembler: hifiasm
      stage: curated
      id: uuid
      pri_fasta: '/path/to/primary_asm-hifiasm-curated-uuid.fasta'
  # Include HiFi reads for Merqury
  hifi:
    - reads: '/path/to/raw/data/hifi/LS_HIFI_R001.bam'

Workflow organization

The workflows in this folder manage the execution of your analyses from beginning to end.

workflow/
 | - .github/                        Github data such as actions to run
 | - assets/                         Workflow assets such as test samplesheets
 | - bin/                            Custom workflow scripts
 | - configs/                        Configuration files that govern workflow execution
 | - dockerfiles/                    Custom container definition files
 | - docs/                           Workflow usage and interpretation information
 | - modules/                        Process definitions for tools used in the workflow
 | - subworkflows/                   Custom workflows for different stages of the main analysis
 | - tests/                          Workflow tests
 | - main.nf                         The primary analysis script
 | - nextflow.config                 General Nextflow configuration
 \ - modules.json                    nf-core file which tracks modules/subworkflows from nf-core