nf-core/coproid
Coprolite host Identification pipeline
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
string^\S+\.csv$Path to comma-separated file containing information about the reference genomes.
string^\S+\.csv$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})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringcoproidOptions to be provided to the pipeline
Used as a prefix for (merged) output reports
stringcoproidPath to a kraken2 database, can be a directory or *.tar.gz
stringSources TAXID count table in csv format for sourcepredict
stringLabels for the sources table in csv format for sourcepredict
stringPath to pre-downloaded ~/.etetoolkit/taxa.sqlite file, if not supplied it will be pulled from the test-data repository
string[:]/genomics/prokaryotes/metagenome/taxonomy/misc/taxa_sqlite.xzPath to pre-downloaded ~/.etetoolkit/taxa.sqlite.traverse.pkl file, if not supplied it will be pulled from the test-data repository
string[:]/genomics/prokaryotes/metagenome/taxonomy/misc/taxa_sqlite_traverse.pklPath to pre-downloaded ~/.sam2lca directory, if not supplied a local database will be build from the reference genomes
stringSam2lca parameter —acc2tax, use default ‘adnamap’ when no sam2lca_db is supplied, change accordingly for sam2lca_db (e.g. ‘nucl’)
stringadnamapSet the sam2lca —identity parameter
number0.9Do not load the iGenomes reference config.
booleantrueThe base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Method used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
booleanIncoming hook URL for messaging service
stringCustom 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).
booleanstringhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/databoolean