WrightonLabCSU/dram pipeline parameters

DRAM (Distilled and Refined Annotation of Metabolism) is a tool for annotating metagenomic assembled genomes

Pipeline Steps

Which steps to run in the pipeline.

Parameter	Description	Type	Default	Required	Hidden
rename	Rename FASTA headers based on file name. Example: sample1.fa –> (fasta header renamed to) > sample1…… Why? DRAM output is focused on scaffolds/contigs with respect to each provided input input_fasta. Thus, without renaming FASTA headers, the individual scaffolds/contigs will not be distinguashable. *If you have already renamed your FASTA headers, do not include with ‘–call’.	boolean
call	Whether to call genes on the input FASTA files using Prodigal.	boolean
annotate	Annotate called genes using downloaded databases.	boolean
qc	Run quality control steps such as collect rRNA and tRNA scans. See QC section for more options.	boolean
summarize	Summarize annotations into a distilled output file. Will use all available topic distillate forms. Ecosystem	boolean
visualize	Generate a product visualization of the annotations and save the output to the output directory.	boolean
traits	Using a DRAM annotations file, make a table of adjectives. Still in development, but can still be used.	boolean
merge_annotations	Path to directory pointing to multiple DRAM annotations to merge into one file. This is ran as a separate pipeline.	string
format_kegg	Format KEGG database for use in DRAM. Standalone operation, will exit after completion.	boolean

Input/output options

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

Parameter	Description	Type	Default	Required	Hidden
outdir	The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.	string		True
input_fasta	Path to FASTA directory Help This parameter is mandatory.	string
fasta_fmt	Input format for the FASTA file.	string	.f
input_genes	Directory containing called genes. Only used when not running call. This allows you to provide pre-called genes to the pipeline.	string
genes_fmt	Input format for the Genes file.	string	*.faa
genes_fna_fmt	Input format for the Genes fna file. Only needed if you are not running call and you are passing --generate_gff or --generate_gbk.	string	*.fna

Call Prodigal Options

Call genes on the input FASTA files using Prodigal.

Parameter	Description	Type	Default	Required	Hidden
prodigal_mode	Mode for Prodigal gene calling.	string	meta
prodigal_trans_table	Translation table to use.	number	11.0
min_contig_len	Minimum contig length in base pairs.	number	2500.0

Annotate Options

Parameter	Description	Type	Default	Required	Hidden
anno_dbs	Alternative way to specify database list for annotation. Comma sepeterated list of databases to include in the annotates. Use all for all. Example: ‘kegg,dbcan,kofam,merops,viral,camper,cant_hyd,fegenie,sulfur,methyl,uniref,pfam,vogdb’. When in doubt, use the name after use_ for each database. This option overrides individual use_ database flags. (WARNING, this option name may change in the future)	string
use_camper	Use the CAMPer database for annotation.	boolean
use_canthyd	Use the Cant_Hyd database for annotation.	boolean
use_dbcan	Use the DBCan database for annotation.	boolean
use_fegenie	Use the FeGenie database for annotation.	boolean
use_kegg	Use the KEGG database for annotation.	boolean
use_kofam	Use the Kofam database for annotation.	boolean
use_merops	Use the MEROPS database for annotation.	boolean
use_methyl	Use the Methyl database for annotation.	boolean
use_pfam	Use the PFAM database for annotation. Currently disabled for this release as a bug was discovered with the pfam DRAM2 implementation. It will be re-enabled in the next release.	boolean
use_sulfur	Use the Sulfur database for annotation.	boolean
use_uniref	Use the UniRef database for annotation.	boolean
use_metals	Use the Metals database for annotation.	boolean
use_vog		boolean
use_viral		boolean			True
add_annotations	Path to old annotations to add to the current run.	string
bit_score_threshold	Minimum BitScore of search to retain hits’)	number	60.0
rbh_bit_score_threshold	Minimum BitScore of reverse best hits to retain hits	number	350.0
database_list	Database list for generating GFF and GBK. Comma sepeterated list of databases to include in the annotates. Use all for all. Example: ‘kegg,dbcan,kofam,merops,viral,camper,cant_hyd,fegenie,sulfur,methyl,uniref,pfam,vogdb’	string	all
generate_gff	Generate GFF output for each input_fasta. This option is in development right now and may not work properly, and may not work with large numbers of inputs.	boolean
generate_gbk	Generate GBK output for each input_fasta. This option is in development right now and may not work properly, and may not work with large numbers of inputs.	boolean

QC Options

Quality control options for DRAM workflow. The QC step collects rRNA and tRNA scans using Barrnap and tRNAscan-SE for the genome_states.tsv output as a baseline. Additional options can be found below.

Parameter	Description	Type	Default	Required	Hidden
bin_quality	Path to bin quality tsv. CheckM and CheckM2 compatible.	string
taxa	Path to bin taxonomy tsv. Compatible with GTDB.	string

Summarize Options

The purpose of DRAM summarize is to distill down annotations based on curated distillation summary form(s). It can be ran with either just –sumarize, or currated sheets with –distill_topic, –distill_ecosystem, or –distill_custom (or some combination). User’s may also provide a custom distillate via –distill_custom <path/to/file> (TSV forms). Summarize can be ran independent of –annotate however, annotations must be provided (–annotations <path/to/annotations.tsv>). Optional tRNA, rRNA and bin quality may also be provided. When using distll, you also must use kegg, ko, dbcan, or merops when you do your annotation. To get the full results, you need to use kegg or ko and dbcan and merops.

Parameter	Description	Type	Default	Required	Hidden
sum_ecos	Ecosystem to distill. Options: <eng_sys	ag> If more than one ecosystem included, they must be seperated by a comma (–sum_ecos eng_sys,ag or –sum_ecos ‘eng_sys,ag’).	string
distill_topic	A way to specify a subset of topics instead of all topics. By default, if --sumarize is specified, all topics are included. Options: <carbon	energy	misc	nitrogen	transport
sum_custom	<path/to/custom_distillate.tsv> Custom distill file to use. The custom distill file must be in TSV format with the first column being the gene ID and the second column being the distillate value.	string
annotations	Path to annotations tsv to distill. Required if running without annotate	string
rrnas	Path to folder containing individual rRNA files generated with tRNAscan-SE. Can be used when running distill without call to add additional information.	string
trnas	Path to folder containging individual tRNA files generated with tRNAscan-SE. Can be used when running distill without call to add additional information.	string
distill_dummy_sheet	File path to distill dummy sheet.	string			True

Product Options

The purpose of DRAM –product is to generate a product visualization of the annotations and save the output to the output directory.

Parameter	Description	Type	Default	Required	Hidden
groupby_column	Column to to group by in the annotations file for etc and function groupings. Defaults to DRAM’s annotation output fasta column name.	string

Adjectives Options

The purpose of DRAM –adjectives is to use the outputted DRAM annotations file to make a table of adjectives. You need to use the Kegg, FeGenie, and Sulfur Databases.

Parameter	Description	Type	Default	Required	Hidden
adjectives_list	A comma seperated list of adjectives (‘adj1,adj2,adj3’), by name, to evaluate. This limits the number of adjectives that are evaluated and is faster.	string
rules_tsv	This is an optional path to a rules file with strict formatting. It will take the place of the original rules file that is stored with the script. For formatting, see the original rules.tsv sheet stored with the script in the repo.	string

Database Options

File paths to databases used in the workflow.

Parameter	Description	Type	Default	Required	Hidden
kegg_db		string	${launchDir}/databases/kegg/		True
uniref_db		string	${launchDir}/databases/uniref/		True
metals_db		string	${launchDir}/databases/metals/		True
pfam_mmseq_db		string	${launchDir}/databases/pfam/mmseqs/		True
merops_db		string	${launchDir}/databases/merops/		True
viral_db		string	${launchDir}/databases/viral/		True
kofam_db		string	${launchDir}/databases/kofam/		True
kofam_list		string	${launchDir}/databases/kofam/kofam_ko_list.tsv		True
dbcan_db		string	${launchDir}/databases/dbcan/		True
dbcan_fam_activities		string	${launchDir}/databases/dbcan/dbcan.fam-activities.tsv		True
dbcan_subfam_activities		string	${launchDir}/databases/dbcan/dbcan.fam-activities.tsv		True
vog_db		string	${launchDir}/databases/vog/		True
vog_list		string	${launchDir}/databases/vogdb/vog_annotations_latest.tsv.gz		True
camper_hmm_db		string	${launchDir}/databases/camper/hmm/		True
camper_hmm_list		string	${launchDir}/databases/camper/hmm/camper_hmm_scores.tsv		True
camper_mmseqs_db		string	${launchDir}/databases/camper/mmseqs/		True
camper_mmseqs_list		string	${launchDir}/databases/camper/mmseqs/camper_scores.tsv		True
canthyd_hmm_db		string	${launchDir}/databases/canthyd/hmm/		True
cant_hyd_hmm_list		string	${launchDir}/databases/canthyd/hmm/cant_hyd_HMM_scores.tsv		True
canthyd_mmseqs_db		string	${launchDir}/databases/canthyd/mmseqs/		True
canthyd_mmseqs_list		string	${launchDir}/databases/canthyd/mmseqs/cant_hyd_BLAST_scores.tsv		True
fegenie_db		string	${launchDir}/databases/fegenie/		True
fegenie_list		string	${launchDir}/databases/fegenie/fegenie_iron_cut_offs.txt		True
sulfur_db		string	${launchDir}/databases/sulfur/		True
methyl_db		string	${launchDir}/databases/methyl/		True
sql_descriptions_db		string	${launchDir}/databases/db_descriptions/description_db.sqlite		True
kegg_e_value		string	1e-05		True
kofam_e_value		string	1e-05		True
dbcan_e_value		string	1e-15		True
merops_e_value		string	1e-1		True
vog_e_value		string	1e-05		True
camper_e_value		string	1e-05		True
uniref_e_value		string	1e-05		True
canthyd_e_value		string	1e-05		True
sulfur_e_value		string	1e-05		True
fegenie_e_value		string	1e-05		True
metals_e_value		string	1e-03		True

Format Kegg Options

Options for preparing the KEGG database for use in DRAM.

Parameter	Description	Type	Default	Required	Hidden
kegg_pep_root_dir	Only required if you need to concatenate all of KEGG’s provided pep files. Root directory to downloaded KEGG peptide files. The pipeline will search for all pep files in this directory and concatenate them into a single file. In format <root_dir>//.pep.	string
kegg_pep_loc	Path to and of the gene fasta files that are provided by the KEGG FTP server or a concatenated version of them. Either this or kegg_pep_root_dir must be provided.	string
gene_ko_link_loc	Path to and of the KO file that is provided by the KEGG FTP server.	string
skip_gene_ko_link	Skip the gene_ko_link file. If you are using an older version of KEGG that does not supply the gene_ko_link file you can use this option to skip the gene_ko_link file. Otherwise, the gene_ko_link file is required.	boolean
kegg_download_date	The date the KEGG database was downloaded. If not provided, the current date will be used.	string	yyyy-MM-dd

SLURM Options

Generic options for SLURM job submission. More customized options can be configured in your own Nextflow config file. See https://www.nextflow.io/docs/latest/executor.html#slurm and example configs here: https://github.com/nf-core/configs/tree/master/conf

Parameter	Description	Type	Default	Required	Hidden
slurm	Launch the pipeline using the SLURM executor. Without this option, the pipeline will run in your current shell/environment.	boolean
partition	Name of the SLURM partition to use for job submission. If not provided, the default partition will be used.	string
slurm_node	Name of the SLURM Node to use for job submission. If not provided, the default node will be used.	string
cpu_provision_limit	The largest numbers of CPUs you can provision in 1 job. Not the total CPU limit. You can control that with process size or provision limit and queue_size	integer
mem_gb_provision_limit	The largest amount of memory you can provision in 1 job. Not the total memory limit. You can control that with process size or provision limit and queue_size	integer
time_hr_provision_limit	The longest time a job should be provisioned for. Not the total length cutoff for all jobs. You can control that with process size or provision limit and queue_size	integer

Process Options

Total resource limits for a single process. Not the limit to the total resources available to the pipeline. Up to queue_size processes can run in parallel, of various sizes

Parameter	Description	Type	Default	Required	Hidden
tiny_cpus_limit	Maximum number of CPUs to use/provision for a this job size.	integer
small_cpus_limit	Maximum number of CPUs to use/provision for a this job size.	integer
medium_cpus_limit	Maximum number of CPUs to use/provision for a this job size.	integer
big_cpus_limit	Maximum number of CPUs to use/provision for a this job size.	integer
huge_cpus_limit	Maximum number of CPUs to use/provision for a this job size.	integer
tiny_gb_mem_limit	Maximum memory to use/provision for a this job size.	integer
small_gb_mem_limit	Maximum memory to use/provision for a this job size.	integer
medium_gb_mem_limit	Maximum memory to use/provision for a this job size.	integer
big_gb_mem_limit	Maximum memory to use/provision for a this job size.	integer
huge_gb_mem_limit	Maximum memory to use/provision for a this job size.	integer
tiny_hr_time_limit	Maximum time in hours to use/provision for a this job size.	integer
small_hr_time_limit	Maximum time in hours to use/provision for a this job size.	integer
medium_hr_time_limit	Maximum time in hours to use/provision for a this job size.	integer
big_hr_time_limit	Maximum time in hours to use/provision for a this job size.	integer
huge_hr_time_limit	Maximum time in hours to use/provision for a this job size.	integer
queue_size	Maximum number of jobs to submit to the queue at once.	integer	10

aliased_options

Aliased options for DRAM annotation workflow. These are provided for backward compatibility with older versions of the pipeline.

Parameter	Description	Type	Default	Required	Hidden
product	alias for visualize.	boolean
adjectives	alias for traits.	boolean
distill_ecosystem	alias for sum_ecos.	string
distill_custom	alias for sum_custom.	string

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, you should download the files from the repo and tell Nextflow where to find them with this parameter.	string	https://raw.githubusercontent.com/nf-core/configs/master		True
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

Generic options

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

Parameter	Description	Type	Default	Required	Hidden
threads		integer	10		True
version	Display version and exit.	boolean			True
publish_dir_mode	Method used to save pipeline results to output directory. Help The Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.	string	copy		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 need to specify this on the command line for every run.	string			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			True
plaintext_email	Send plain-text email instead of HTML.	boolean			True
max_multiqc_email_size	File size limit when attaching MultiQC reports to summary emails.	string	25.MB		True
monochrome_logs	Do not use coloured log outputs.	boolean			True
hook_url	Incoming hook URL for messaging service Help Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.	string			True
multiqc_title	MultiQC report title. Printed as page header, used for filename if not otherwise specified.	string			True
multiqc_config	Custom config file to supply to MultiQC.	string			True
multiqc_logo	Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file	string			True
multiqc_methods_description	Custom MultiQC yaml file containing HTML including a methods description.	string
validate_params	Boolean whether to validate parameters against the schema at runtime	boolean	True		True
pipelines_testdata_base_path	Base URL or local path to location of pipeline test dataset files	string	https://raw.githubusercontent.com/nf-core/test-datasets/		True
trace_report_suffix	Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.	string	yyyy-MM-dd_HH-mm-ssZ		True