nf-core/seqsubmit
nf-core pipeline for data submission to ENA
Define where the pipeline should find input data and save output data.
Path to samplesheet describing the data to be submitted (supported formats: csv, tsv, yaml, yml, json). Columns/fields depend on the pipeline mode
string^\S+\.(csv|tsv|yaml|yml|json)$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringParameters affecting a decision about presence/absence of tRNA and rRNA genes (RNA_presence) in a genome
Minimum percentage of 16S, 23S, and 5S rRNA gene length recovered to count the gene as present.
number80Minimum number of tRNA genes detected to count tRNA as present. This value is defined by the MISAG/MIMAG standard and must not be modified.
number18CAT_pack required data
Path to local CAT_pack DB
Parameters used to run Checkm2
Path to pre-downloaded CheckM2 database. If omitted, downloads the version set by --checkm2_db_download_id
Zenodo ID for CheckM2 database download
integer14897628Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
stringDisplay the help message.
boolean,stringDisplay the full detailed help message.
booleanDisplay hidden parameters in the help message (only works when –help or –help_full are provided).
booleanUse these parameters to control the flow of the pipeline execution.
Name of the submitter’s organisation (mandatory for broker accounts).
stringMark the assemblies as a Third PArty (TPA)
booleanType of the data to be submitted
stringUpload to ENA TEST server instead of LIVE server
booleantrueUse that flag if you are referencing private data accessions in the samplesheet
booleanDate (YYYY-MM-DD) until which the newly created study stays private in ENA.
string^\d{4}-\d{2}-\d{2}$ENA study accession (PRJ/ERP) to submit the data to
stringPath to a file (JSON, CSV, or TSV) with metadata for registering a new ENA study. Required if –submission_study is not set.
stringWebin-CLI mode for ENA interaction: submit uploads data, validate performs validation only.
string