parameters.md

socialgene/sgnf pipeline parameters

Scalable genome mining with SocialGene knowledge graphs

Input Genomes

Any one or more of the following can be used to download/input genomes for the pipeline

Parameter	Description	Type	Default	Required	Hidden
ncbi_genome_download_command	Arguments to pass to ncbi_genome_download_command Help See the following link for more info about commands you can use: https://github.com/kblin/ncbi-genome-download	string
ncbi_datasets_command	Taxonomic name (maybe NCBI taxonomy id as well?) see extended help before using Help Note/Warning: Specifying a taxon directly has the potential to download a large number of genomes that you may not be prepared to handle.
ncbi_datasets_file	Instead of using the 'ncbi_datasets_command', the path to a file of NCBI genome accessions to download can provided (single accessio per line)	string
local_genbank	Path to local GenBank file(s), can be a glob Help Accepted files: gbff, gbk and gzipped versions of those	string
local_faa	Path to local protein FASTA file(s), can be a glob	string
paired_omics_json_path	Paired omics json file, downloaded from: https://pairedomicsdata.bioinformatics.nl/projects	string			True
mibig	Set to true to download and include all MIBiG BGCs as input	boolean
genbank_input_buffer	How many genbank files will be processed in a single task Help Decides how many parallel processes will be used for genbank parsing; number of spawned parse processes = (# of input genomes) / (genbank_input_buffer)</det

Required Output Directories

Define where the pipeline should find input data and save output data.

Parameter	Description	Type	Default	Required	Hidden
outdir	If set, and others not, all other outdirs within this directory	string	socialgene_results	True
outdir_download_cache	Long term caching directory for use between different pipeline runs.	string	socialgene_downloads	True

Input HMMs

Any one or more of the following can be used to download/input HMMs for the pipeline

Parameter	Description	Type	Default	Required	Hidden
custom_hmm_file	File path of a custom HMMER hmm file	string
hmmlist	["all"] or some combination of ["antismash","amrfinder","bigslice","classiphage","pfam","prism","resfams","tigrfam","virus_orthologous_groups"]	array
domtblout_path	Use externally-generated domtblout files. Please read the long description before using Help Use externally-generated domtblout files. The models have to have the same name (identifier) as SocialGene expects, which is a SocialGene-

Optional directory settings

These directories have defaults based on the --outdir parameter, change them if you want

Parameter	Description	Type	Default	Required	Hidden
outdir_per_run	Directory that holds data generated each run	string	socialgene_results/socialgene_per_run		True
outdir_neo4j	Path to the output directory where the results will be saved.	string	socialgene_results/socialgene_neo4j		True
outdir_blast_cache	Cache folder where blast results are written to. Important to delete if starting a new pipeline run with different input data but using same cache directory as a previous run.	string	socialgene_results/socialgene_per_run/blastp_cache		True
outdir_genomes	Storage directory for downloaded genomes	string	socialgene_results/outdir_genomes		True

SocialGene parameters

Parameter	Description	Type	Default	Required	Hidden
fasta_splits	Split non-redundant protein sequences into n-FASTA files Help Use this to run HMMER in parallel/make things faster. Determines how many FASTA files should be the created from all non-redundant protein sequences	`integ
hmm_splits	For most use cases keep this at 1 and increase fasta_splits instead Help Determines how many hmm files should be created to run in parallel. This is mainly for making smaller files for massively parallel distribution on CHTC</deta

SocialGene modules

These determine the annotations and structure of the resulting database

Parameter	Description	Type	Default	Required	Hidden
build_database	Should the Neo4j databse be created?	boolean	True
mmseqs2	Run MMseqs2 on the input proteins? Help https://github.com/soedinglab/MMseqs2	boolean
blastp	Should all vs all BLASTp be run? DO NOT RUN ON LARGE INPUT DATA WITHOUT STRICT FILTERS	boolean
ncbi_taxonomy	Download and insert the NCBI taxonomy database? Requires input assemblies to have NCBI Assembly accessions	boolean
antismash	Run antismash on all input genomes	boolean
chembl	Include chembl data into database Not yet implemented	boolean			True
paired_omics	Not yet implemented	boolean			True

Max job resource request options

Set the top limit for requested resources for any single job.

Parameter	Description	Type	Default	Required	Hidden
max_cpus	Maximum number of CPUs that can be requested for any single job. Help Used to set an upper-limit for the number of CPUs that can be used at once. Should be an integer e.g. --max_cpus 1 https://www.nextflow.io/docs/latest/process.ht
max_memory	Maximum amount of memory that can be requested for any single job. Help Used to set an upper-limit for the memory any single process can use. Should be a string in the format integer-unit e.g. --max_memory '8.GB' https://www.nex
max_time	Maximum amount of time that can be requested for any single job. Help Used to set an upper-limit for the amount of time any single process is allowed to run. Should be a string in the format integer-unit e.g. --max_time '2.h' https
slurm_queue_size	Number of slurm jobs that can be running/submitted	integer	15		True

External Data Versions

Parameter	Description	Type	Default	Required	Hidden
amrfinder_version	Version of amrfinder to download/use	string	2021-03-01.1		True
bigslice_version	Version of bigslice to download/use	string	v1.0.0/bigslice-models.2020-04-27		True
vog_version	Version of vog to download/use	string	vog211		True
tigrfam_version	Version of tigrfam to download/use	string	15.0		True
pfam_version	PFAM version. Ffor version numbers see: http://ftp.ebi.ac.uk/pub/databases/Pfam/releases	string	35.0		True
antismash_hmms_git_sha	Controls which version of antismash the antismash HMMS are pulled from	string	e2d777c6cd035e6bf20f7eec924a350b00b84c7b		True
chembl_version	Set (e.g. 31 for chembl version 31) to incorporate chembl into the database	string	None

HMMER Options

Parameter	Description	Type	Default	Required	Hidden
hmmsearch_model_threshold	--cut_ga or --cut_nc or --cut_tc Help From HMMER documentation: Options controlling model-specific thresholding: --cut_ga : use profile's GA gathering cutoffs to set all thresholding --cut_nc : use profile'
HMMSEARCH_Z	see pg 74-77: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf	integer	100000000		True
HMMSEARCH_IEVALUE	see pg 74-77: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf	number	0.1		True
HMMSEARCH_E	see pg 74-77: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf	number	10		True
HMMSEARCH_DOME	see pg 74-77: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf	number	10		True
HMMSEARCH_INCE	see pg 74-77: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf	number	0.1		True
HMMSEARCH_INCDOME	see pg 74-77: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf	number	0.01		True
HMMSEARCH_SEED	see pg 74-77: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf	integer	42		True
HMMSEARCH_F1	see pg 74-77: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf	number	0.02		True
HMMSEARCH_F2	see pg 74-77: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf	number	0.001		True
HMMSEARCH_F3	see pg 74-77: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf	number	1e-05		True

HTCONDOR specific parameters

These parameters are specific to UW-Madison's CHTC high throuput computing cluster

Parameter	Description	Type	Default	Required	Hidden
htcondor	Use the --htcondor flag to create files for htcondor, then run again with the results from the external run Help When --htcondor is set the pipeline will only run the steps required to generate and split the non-redundant FASTA file and HMM
htcondor_request_memory	See: https://chtc.cs.wisc.edu/uw-research-computing/helloworld	string	1GB		True
htcondor_request_cpus	See: https://chtc.cs.wisc.edu/uw-research-computing/helloworld	integer	1		True
htcondor_request_disk	See: https://chtc.cs.wisc.edu/uw-research-computing/helloworld	string	5GB		True
htcondor_max_idle	See: https://chtc.cs.wisc.edu/uw-research-computing/helloworld	integer	100		True
htcondor_squid_username	See: https://chtc.cs.wisc.edu/uw-research-computing/file-avail-squid	string	cmclark8		True
htcondor_WantGlideIn	See: https://chtc.cs.wisc.edu/uw-research-computing/helloworld	boolean	True		True
htcondor_WantFlocking	See: https://chtc.cs.wisc.edu/uw-research-computing/helloworld	boolean	True		True
htcondor_prep_directory	Where data to be sent to CHTC will be written	string	socialgene_results/htcondor_cache		True

MULTIQC

Parameter	Description	Type	Default	Required	Hidden
multiqc_title	x	string
multiqc_logo	x	string
multiqc_config	x	string
max_multiqc_email_size	x	string	25.MB
multiqc_methods_description	x	string

Generic options

Less common options for the pipeline, typically set in a config file.

Parameter	Description	Type	Default	Required	Hidden
help	Display help text.	boolean			True
email_on_fail	Email address for completion summary, only when pipeline fails. Help An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.	string
plaintext_email	Send plain-text email instead of HTML.	boolean			True
monochrome_logs	Do not use coloured log outputs.	boolean			True
tracedir	Directory to keep pipeline Nextflow logs and reports.	string	${params.outdir}/pipeline_info		True
validate_params	Boolean whether to validate parameters against the schema at runtime	boolean	True		True
show_hidden_params	Show all params when using --help Help By default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.<
hook_url	x	string	None		True
version	Display version and exit.	boolean			True
email	Email address for completion summary. Help Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't nee
fasta	not used, required by nf-core linter	string	not-used-but-needed-in-lint		True
input	not used, required by nf-core linter	string	not-used-but-needed-in-lint		True
sort_fasta	BLAST (and maybe MMseqs2?) differ based on sequence order, setting this to true will sort the protein fasta file first (note: this will make a copy of the data)	boolean			True

Institutional config options

Parameters used to describe centralised config profiles. These should not be edited.

Parameter	Description	Type	Default	Required	Hidden
custom_config_version	Git commit id for Institutional configs.	string	master		True
custom_config_base	Base directory for Institutional configs. Help If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them
config_profile_name	Institutional config name.	string			True
config_profile_description	Institutional config description.	string			True
config_profile_contact	Institutional config contact information.	string			True
config_profile_url	Institutional config URL link.	string			True