andyngh/noHiC-Snakemake

A Snakemake reimplementation of noHiC - the personalized reference-guided contig scaffolding pipeline

Overview

Latest release: v1.1.0, Last update: 2026-09-27

Share link: https://snakemake.github.io/snakemake-workflow-catalog?wf=andyngh/noHiC-Snakemake

Quality control: linting: failed formatting: failed

Deployment

Step 1: Install Snakemake and Snakedeploy

Snakemake and Snakedeploy are best installed via the Conda package manager. It is recommended to install conda via Miniforge. Run

conda create -c conda-forge -c bioconda -c nodefaults --name snakemake snakemake snakedeploy

to install both Snakemake and Snakedeploy in an isolated environment. For all following commands ensure that this environment is activated via

conda activate snakemake

For other installation methods, refer to the Snakemake and Snakedeploy documentation.

Step 2: Deploy workflow

With Snakemake and Snakedeploy installed, the workflow can be deployed as follows. First, create an appropriate project working directory on your system and enter it:

mkdir -p path/to/project-workdir
cd path/to/project-workdir

In all following steps, we will assume that you are inside of that directory. Then run

snakedeploy deploy-workflow https://github.com/andyngh/noHiC-Snakemake . --tag v1.1.0

Snakedeploy will create two folders, workflow and config. The former contains the deployment of the chosen workflow as a Snakemake module, the latter contains configuration files which will be modified in the next step in order to configure the workflow to your needs.

Step 5: Generate report

After finalizing your data analysis, you can automatically generate an interactive visual HTML report for inspection of results together with parameters and code inside of the browser using

snakemake --report report.zip

Configuration

The following section is imported from the workflow’s config/README.md.

Configuration

Conventions for parsing command-line (CI) arguments

Follow these conventions when parsing the CI arguments:

Switch arguments take "yes" / "no" to turn an option or a computational task on/off.
[chained] arguments in an assembly stage are filled in automatically from the preceding stage or from the [global] section. Leave them as "". Only fill in one of these arguments if you want to use a different input file; your manually provided inputs always take precedence over the defaults.
[Required] arguments must be filled in manually.
We highly recommend using absolute paths when filling in your inputs.
You must use distinct output directory names for the five assembly stages of the workflow (refpick, refpolish, clean, asm, and eval).

Section 1. `[stages]` - Choose which sub-workflows to run

Config keys	CI arguments	Main tasks
`refpick`	`run_refpick`	Build (and patch) the synref using the provided pangenome graph (default: yes).
`refpolish`	`run_refpolish`	Polish the synref or a real reference genome (default: yes).
`clean`	`run_clean`	Decontaminate the target contig assembly (default: yes).
`asm`	`run_asm`	Correct and scaffold the target contig assembly (default: yes).
`eval`	`run_eval`	Check the quality of the final assembly (default: yes).

A stage set to "yes" must have its own [Required] arguments filled in.

Section 2. `[global]` - Inputs shared by several stages

Config keys	CI arguments	Notes
`nohic_env_path`	`env`	Path to the downloaded noHiC environment containing the tools (automatically filled in by `setup.sh`).
`reads`	`reads`	[Required] Path to your error-corrected long reads (`.fastq`, may be gzipped).
`sequencing_platform`	`platform`	Your sequencing platform. Fill in one of the following values: `clr`, `hifi`, `ont`, `corrected_clr`, `corrected_ont` (default: hifi).
`sequencing_coverage`	`cov`	The estimated sequencing coverage (int). Default: 10.
`prefix`	`prefix`	[Required] Fill in your output prefix.

Section 3. `[refpick]` - Building the synref for your target genome

Config keys	CI arguments	Description
`seq_file`	`pk_seq`	[chained] Reads for k-mer counting; defaults to `global: reads`. You can also fill in the path to a FASTA file containing the contigs of your target genome.
`kmer_length`	`pk_k`	K-mer length (bp) for KMC-based k-mer counting (default: 29).
`memory`	`pk_mem`	Memory (in GB) for KMC-based k-mer counting (default: 32).
`kmc_mode`	`pk_kmc_mode`	Depends on `seq_file`. Fill in `"fq"` for FASTQ input or `"fm"` for FASTA input (default: fq).
`prefix`	`pk_prefix`	[chained] Set outputs’ prefix. Take “global: prefix” by default.
`kmc_out_dir`	`pk_out`	Output directory of the `nohic-refpick` stage. Must be unique across stages (default: Refpick.outdir).
`kmc_threads`	`pk_kmc_t`	Number of threads for KMC (default: 1). This argument is filled automatically via the `--cores` or `--local-cores` arguments of snakemake
`gbz`	`pk_gbz`	[Required] Path to a pangenome graph in GBZ format.
`hapl`	`pk_hapl`	[Required] Path to the `.hapl` index of your pangenome graph.
`vg_threads`	`pk_vg_t`	Number of threads for the haplotype sampling and synref extraction steps (default: 1). This argument is filled automatically via the `--cores` or `--local-cores` arguments of snakemake
`patch_synref`	`pk_patch`	Fill in `"yes"` or `"no"`. Patches the synref using sequence from a donor genome (default: no).
`donor_genome`	`pk_donor`	Required when `pk_patch=yes`. Path to a high-quality donor genome for synref patching (ideally a gapless genome).
`patch_threads`	`pk_patch_t`	Number of threads for synref patching (default: 1). This argument is filled automatically via the `--cores` or `--local-cores` arguments of snakemake

Section 4. `[refpolish]` - Polishing your reference genome

Config keys	CI arguments	Description
`synref`	`pl_ref`	[chained] Takes the synref from `nohic-refpick` by default. You can also fill in the path to your own reference genome.
`mapping_preset`	`pl_preset`	minimap2 preset used to map the reads of your target genome to the reference. Values can be `map-pb`, `map-hifi`, `map-ont`, or `map-iclr` (default: map-hifi).
`threads`	`pl_t`	Number of threads for `nohic-refpolish` (default: 1). This argument is filled automatically via the `--cores` or `--local-cores` arguments of snakemake
`polish_tool`	`pl_tool`	The polishing tool to use. Fill in either `"hypo"` or `"racon"` (default: `"hypo"`).
`coverage`	`pl_cov`	[chained] The estimated coverage of the reads on the reference genome. Used when `polish_tool: "hypo"`. By default, take sequencing coverage from “global: sequencing_coverage”.
`genome_size`	`pl_gsize`	[Required] The estimated reference genome size (e.g., `"720m"`, `"1g"`). Required when `polish_tool: "hypo"`.
`out_dir`	`pl_out`	Output directory of the `nohic-refpolish` stage (default: Refpolish.outdir).
`prefix`	`pl_prefix`	[chained] Basename of the polished reference. Take “global: prefix” by default.

Section 5. `[clean]` - Decontaminating your target contig assembly

Config keys	CI arguments	Description
`contig_assembly`	`cl_ctg`	[Required] Path to the target contig assembly to clean. Its basename (i.e., without `.fa`/`.fasta`/`.fna`) becomes the sample name used in every output file of this stage.
`out_dir`	`cl_out`	Output directory of the `nohic-clean` stage (default: Clean.outdir).
`adapters`	`cl_adapters`	[Required] Path to a FASTA file containing the adapter sequences to screen for.
`adapter_detection_thread`	`cl_adapter_t`	Number of threads for the adapter detection step (default: 1). This argument is filled automatically via the `--cores` or `--local-cores` arguments of snakemake.
`kraken2_db`	`cl_k2db`	[Required] Path to a downloaded Kraken2 database directory. Fill in `/dev/shm` if `cl_k2_mmap=yes`; in this case, the downloaded Kraken2 database files (`*.k2d`) must be in `/dev/shm`.
`kraken2_thread`	`cl_k2_t`	Number of threads for Kraken2 (default: 1). This argument is filled automatically via the `--cores` or `--local-cores` arguments of snakemake.
`kraken2_memory_mapping`	`cl_k2_mmap`	Fill in `"yes"` to use Kraken2’s memory-mapping mode or `"no"` to turn this mode off (default: no).
`taxonomic_group`	`cl_taxon`	The clade to keep. Contigs whose Kraken2 lineage does not contain this string are treated as contaminants. (default: Viridiplantae).
`org_ctg_identification`	`cl_org`	Fill in `"yes"` to remove organellar (mitochondrial/plastid) contigs via BLASTn or `"no"` to turn this step off (default: no).
`reference_organellar_sequences`	`cl_org_ref`	Required when `cl_org=yes`. Path to a FASTA file containing the reference organellar sequences used as the BLAST database.
`blastn_thread`	`cl_blast_t`	Number of threads for BLASTn (default: 1). This argument is filled automatically via the `--cores` or `--local-cores` arguments of snakemake.

[!NOTE] The adapter check is a hard gate: if any adapter is found in your contigs, the workflow stops and points you to 1_adapter_check/{sample}.adapter_positions.bed.

Section 6. `[asm]` - Target contig correction, scaffolding, and gap closing

Config keys	CI arguments	Description
`contigs`	`as_ctg`	[chained] Takes the decontaminated contigs from `nohic-clean` by default.
`reference_genome`	`as_ref`	[chained] Takes the polished synref from `nohic-refpolish` (or the synref from `nohic-refpick` if `nohic-refpolish` is off) by default. You can also specify the path to a real reference genome here.
`out_dir`	`as_out`	Output directory of the `nohic-asm` stage (default: Asm.outdir).
`out_prefix`	`as_prefix`	[chained] Basename of the outputs. Take “global: prefix” by default.
`run_craq`	`as_craq`	Fill in `"yes"` to turn on CRAQ-based chimeric contig breaking or `"no"` to turn this step off (default: yes).
`craq_threads`	`as_craq_t`	Number of threads for CRAQ; should be 5–6 lower than for the other steps (default: 1). This argument is filled automatically via the `--cores` or `--local-cores` arguments of snakemake.
`ignore_het`	`as_ignore_het`	Filling in `"yes"` lowers the CRAQ clipped-read threshold from 0.75 to 0.55. Use it when your contigs contain many heterozygous misjoins. Fill in `"no"` to use the default value (0.75) (default: no).
`run_inspector`	`as_inspector`	Fill in `"yes"` to turn on Inspector-based misassembly detection and correction or `"no"` to turn this step off (default: yes).
`inspector_threads`	`as_inspector_t`	Number of threads for Inspector (default: 1). This argument is filled automatically via the `--cores` or `--local-cores` arguments of snakemake.
`run_ragtag_correct`	`as_ragtag`	Fill in `"yes"` to turn on reference-guided contig correction with `RagTag correct` or `"no"` to turn this step off (default: yes).
`ragtag_threads`	`as_ragtag_t`	Number of threads for `RagTag correct` and `RagTag scaffold` (default: 1). This argument is filled automatically via the `--cores` or `--local-cores` arguments of snakemake.
`preset`	`as_preset`	Aggressiveness of `RagTag correct`. See the table below (default: `"luck"`).
`run_gap_closing`	`as_gapclose`	Fill in `"yes"` to turn on TGS-GapCloser or `"no"` to turn this step off (default: yes).
`gap_closing_threads`	`as_gapclose_t`	Number of threads for gap closing (default: 1). This argument is filled automatically via the `--cores` or `--local-cores` arguments of snakemake.

`RagTag correct` presets

See the detailed descriptions of the presets in our preprint.

`preset`	Behavior	Use case
`draft`	Uses the default settings of `RagTag correct`.	When you want an initial assembly without much correction.
`luck`	Sets the window size for read-based misassembly validation to 45000 and removes short alignments (< 1000 bp) between the target contigs and the reference genome (default preset).	A balanced preset for when you want more aggressive contig correction but don’t want to force the target genome’s sequence structure to follow the reference genome too closely.
`standard`	Similar to `luck`, but uses `nucmer` to align your contigs to the reference genome.	Use this preset when you have a high-quality (possibly gapless/T2T) reference genome that is genetically close to your target genome, because this preset strictly forces the sequence structure of the target genome to follow the reference.
`aggressive`	Similar to `standard`, but with a lower alignment merging distance of 50000 bp.	Even stricter than `standard`. Use it only when you detect misjoins in your contigs that are very hard to break.
`raw`	`nucmer` aligner with no read validation.	Use this preset when you want to break the contigs at every point where they disagree with the reference genome (not recommended).

[!NOTE] RagTag correct only accepts hifi, ont, corrected_clr, or corrected_ont as the sequencing platform; raw clr is not supported by this step.

Section 7. `[eval]` - Final assembly QC

Config keys	CI arguments	Description
`assembly`	`ev_asm`	[chained] Takes the final assembly from `nohic-asm` by default.
`reference_genome`	`ev_ref`	[chained] Takes the synref from `nohic-refpick` or `nohic-refpolish` by default. You can also fill in the path to a real reference genome to compare against. Required when QUAST or the dot plot visualization is enabled.
`out_dir`	`ev_out`	Output directory of the `nohic-eval` stage (default: Eval.outdir).
`contiguity_evaluation_tool`	`ev_contig_tool`	The tool used to calculate contiguity metrics. Fill in `"gfastats"`, `"quast"`, or `"no"` (to turn this step off). Use `"gfastats"` when you don’t need the NGA50 and auNGA values. Default: quast.
`contiguity_threads`	`ev_contig_t`	Number of threads for the contiguity metric calculations (default: 1). This argument is filled automatically via the `--cores` or `--local-cores` arguments of snakemake.
`gene_space_compl_eval_tool`	`ev_gene_tool`	The tool used to evaluate gene-space completeness. Fill in `"compleasm"` (recommended), `"busco"`, or `"no"` (to turn this step off). Default: compleasm.
`gene_space_compl_eval_threads`	`ev_gene_t`	Number of threads for the gene-space completeness evaluation (default: 1). This argument is filled automatically via the `--cores` or `--local-cores` arguments of snakemake.
`lineage`	`ev_lineage`	The BUSCO/compleasm lineage, e.g., `"poales"`, `"embryophyta"`, … (default: `eukaryota`).
`odb`	`ev_odb`	The OrthoDB release (default: `"odb12"`).
`busco_out_prefix`	`ev_busco_prefix`	[chained] Output prefix for BUSCO. Used when `gene_space_compl_eval_tool: "busco"`. Take “global: prefix” by default.
`run_craq`	`ev_craq`	Fill in `"yes"` to turn on CRAQ-based evaluation (to obtain the R- and S-AQI values) or `"no"` to turn this step off (default: yes).
`craq_threads`	`ev_craq_t`	Number of threads for CRAQ; should be 5–6 lower than for the other steps (default: 1). This argument is filled automatically via the `--cores` or `--local-cores` arguments of snakemake.
`run_inspector`	`ev_inspector`	Fill in `"yes"` to obtain the Inspector QV and misassembly report or `"no"` to turn this step off (default: yes).
`inspector_threads`	`ev_inspector_t`	Number of threads for Inspector (default: 1). This argument is filled automatically via the `--cores` or `--local-cores` arguments of snakemake.
`run_viz`	`ev_viz`	Fill in `"yes"` to draw a dot plot of the target assembly against the reference or `"no"` to turn this step off (default: yes).
`minimap2_preset`	`ev_mm2_preset`	minimap2 preset for the dot plot mapping (default: `asm5`).
`viz_threads`	`ev_viz_t`	Number of threads for the dot plot visualization (default: 1). This argument is filled automatically via the `--cores` or `--local-cores` arguments of snakemake.

[!NOTE] compleasm is run from a sibling environment of nohic_env_path: if the environment is /path/to/noHiC-Snakemake/workflow/envs/noHiC, compleasm is expected at /path/to/noHiC-Snakemake/workflow/envs/compleasm. BUSCO runs from the main noHiC environment.

Using SLURM in `nohic-eval`

Only the evaluation stage submits jobs. use_slurm: "yes" attaches SLURM resources to its heavy rules. Use the following CI arguments for SLURM setting.

CI arguments	Defaults	Descriptions
`ev_slurm`	no	Fill in “yes” or “no” to use SLURM.
`slurm_mem`	250G	Set the memory requirement for SLURM jobs (e.g., “32000M” or “32G”).
`slurm_partition`	‘’	Set the SLURM partition. Leave it empty (“”) to let the SLURM site default decide.
`slurm_account`	‘’	Set the SLURM account. “” if your cluster does not use accounts.
`slurm_time`	24h	Set the wall time for each evaluation step (e.g., “4h”, “2d”; “” = partition default).

The above settings are for all steps of nohic-eval. You can also set the resource requirements specifically for a step. Check the help message for details.

snakemake -s /path/to/noHiC-Snakemake/workflow/Snakefile --config help=yes

Linting and formatting

Linting results

/home/runner/work/snakemake-workflow-catalog/snakemake-workflow-catalog/.pixi/envs/default/lib/python3.13/site-packages/google/auth/transport/grpc.py:43: FutureWarning: grpcio < 1.83.0 does not support Post-Quantum Cryptography (PQC). Support for non-PQC environments is deprecated. In April 2027, google-auth will raise its minimum requirements to enforce grpcio >= 1.83.0. For more details on Google Cloud's post-quantum security migration, visit: https://cloud.google.com/security/resources/post-quantum-cryptography
  warnings.warn(
Using workflow specific profile profiles/default for setting default command line arguments.
noHiC: threads from --cores: 1 (CRAQ: 1)
WorkflowError in file "/tmp/tmpn7s3sbc9/andyngh-noHiC-Snakemake-c487035/workflow/Snakefile", line 568:
ERROR: the following keys are missing from the config file.
Keys that are normally filled in by an earlier stage have to be given
by hand when that stage is switched off in 'stages:'.
  refpick: seq_file
  refpick: prefix
  refpick: gbz
  refpick: hapl
  refpolish: reads
  refpolish: prefix
  clean: contig_assembly
  clean: adapters
  clean: kraken2_db
  asm: out_prefix
  asm: reads
  eval: reads
  File "/tmp/tmpn7s3sbc9/andyngh-noHiC-Snakemake-c487035/workflow/Snakefile", line 568, in <module>

Formatting results

[DEBUG] 
[DEBUG] In file "/tmp/tmpn7s3sbc9/andyngh-noHiC-Snakemake-c487035/workflow/rules/nohic-eval.slurm.c.smk":  Formatted content is different from original
[DEBUG] 
[DEBUG] In file "/tmp/tmpn7s3sbc9/andyngh-noHiC-Snakemake-c487035/workflow/rules/nohic-clean.c.smk":  Formatted content is different from original
[DEBUG] 
[DEBUG] In file "/tmp/tmpn7s3sbc9/andyngh-noHiC-Snakemake-c487035/workflow/Snakefile":  Formatted content is different from original
[DEBUG] 
[DEBUG] In file "/tmp/tmpn7s3sbc9/andyngh-noHiC-Snakemake-c487035/workflow/rules/nohic-refpick.c.smk":  Formatted content is different from original
[DEBUG] 
[DEBUG] In file "/tmp/tmpn7s3sbc9/andyngh-noHiC-Snakemake-c487035/workflow/rules/nohic-refpolish.c.smk":  Formatted content is different from original
[DEBUG] 
[DEBUG] In file "/tmp/tmpn7s3sbc9/andyngh-noHiC-Snakemake-c487035/workflow/rules/nohic-asm.c.smk":  Formatted content is different from original
[INFO] 6 file(s) would be changed 😬

snakefmt version: 0.11.5

andyngh/noHiC-Snakemake

Overview

Deployment

Configuration

Configuration

Conventions for parsing command-line (CI) arguments

Section 1. [stages] - Choose which sub-workflows to run

Section 2. [global] - Inputs shared by several stages

Section 3. [refpick] - Building the synref for your target genome

Section 4. [refpolish] - Polishing your reference genome

Section 5. [clean] - Decontaminating your target contig assembly

Section 6. [asm] - Target contig correction, scaffolding, and gap closing

RagTag correct presets

Section 7. [eval] - Final assembly QC

Using SLURM in nohic-eval

Linting and formatting

Section 1. `[stages]` - Choose which sub-workflows to run

Section 2. `[global]` - Inputs shared by several stages

Section 3. `[refpick]` - Building the synref for your target genome

Section 4. `[refpolish]` - Polishing your reference genome

Section 5. `[clean]` - Decontaminating your target contig assembly

Section 6. `[asm]` - Target contig correction, scaffolding, and gap closing

`RagTag correct` presets

Section 7. `[eval]` - Final assembly QC

Using SLURM in `nohic-eval`