nf-core/fastquorum
Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)
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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringMost common options used for the pipeline
The pipeline mode to use, either 'rd' for R&D or 'ht' for High-Throughput
stringEnable when the input is duplex sequenecing.
booleanWith this parameter flags in various tools are set for duplex sequencing data.
Options for when grouping reads by UMI
Grouping strategy
stringGrouping strategy for fgbio's GroupReadsByUmi. (options: Identity, Edit, Adjacency, Paired, Default). Using an empty string will default to 'Paired' for duplex sequencing data, and 'Adjacency' otherwise.
Maximum number of edits
integerMaximum number of allowable edits for fgbio's GroupReadsByUmi.
Options for when creating consensus reads
Minimum reads to call a consensus
integer,stringThe minimum reads to call a consensus for fgbio's CallMolecularConsensusReads/CallDuplexConsensusReads.
Minimum input base quality
integerThe minimum input base quality to use when calling a consensus for fgbio's CallMolecularConsensusReads/CallDuplexConsensusReads.
Options for when filtering consensus reads
Minimum reads to keep a consensus
integer,stringThe minimum reads to keep a consensus for fgbio's FilterConsensusReads.
Minimum consensus base quality
integerThe minimum consensus base quality to keep when calling a consensus for fgbio's FilterConsensusReads.
The maximum error rate for a single consensus base
number,stringThe maximum error rate for a single consensus base when filtering a consensus for fgbio's FilterConsensusReads.
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
stringIf using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.
See the nf-core website docs for more details.
Path to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
Path to FASTA dictionary file.
stringIf you use AWS iGenomes, this has already been set for you appropriately.
NB If none provided, will be generated automatically from the FASTA reference. Combine with
--save_referenceto save for future runs.
Path to FASTA reference index.
stringIf you use AWS iGenomes, this has already been set for you appropriately.
NB If none provided, will be generated automatically from the FASTA reference. Combine with
--save_referenceto save for future runs.
Path to BWA mem indices.
stringIf you use AWS iGenomes, this has already been set for you appropriately.
If you wish to recompute indices available on igenomes, set --bwa false.
NB If none provided, will be generated automatically from the FASTA reference. Combine with
--save_referenceto save for future runs.
Do not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
If generated by the pipeline save the STAR index in the results directory.
booleanIf an alignment index is generated by the pipeline use this parameter to save it to your results folder. These can then be used for future pipeline runs, reducing processing times.
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/masterIf 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.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
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
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom 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.
stringTwo-column sample renaming TSV file passed to MultiQC. First column a set of patterns, second column a set of corresponding replacements.
stringTSV file with headers passed to MultiQC.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanBy 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.
Validation of parameters fails when an unrecognised parameter is found.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.