nf-core/hgtseq
A pipeline to investigate horizontal gene transfer from NGS data
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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringTaxID of samples used as input
numberEmail address for completion summary.
stringMultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringIndicates if input files are BAMs: if not, FASTQ files are assumed and alignment is run
booleanDefines if pipeline is running a test or using full scale inputs
booleanChoose if aligner should be bwa-mem or bwa-mem2
stringbwa-memChoose if multiqc has data to add kraken to report
booleantrueReference genome related files and options required for the workflow
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/Do not load the iGenomes reference config.
booleanA local path to kraken database folder or compressed database file, or a URL to a compressed database file, in tar.gz format
stringA local path or a URL to a .tab krona taxonomy file; it can also receive a compressed .tab file in tar.gz format
stringPath to GFF/GTF annotation file.
stringPath bwa-mem indexes
stringPath bwa-mem2 indexes
stringParameters 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.
stringcopyEmail 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.MBDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringBoolean whether to validate parameters against the schema at runtime
booleantrueSuffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
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.
stringPath to nf-core/test-datasets
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/