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.

required
type: string
pattern: ^\S+\.csv$

Specify input format. Default FASTQ. Options ‘FASTQ’ or ‘BAM’.

required
type: string

Specify if bam file is sorted [false, true]. If false or not specified, bam file will be sorted!

type: boolean

Specify if sorted bam file should be saved [false, true]. Default: false

type: boolean

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

required
type: string

Email address for completion summary.

type: string
pattern: ^([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.

type: string

Options to adjust inital circular DNA identifier

Specifies the circular DNA identification algorithm to use - available ‘circle_map_realign’, ‘circle_map_repeats’, ‘circle_finder’, ‘circexplorer2’, and ‘ampliconarchitect’. Multiple circle_identifier’s can be specified with a comma-separated string. E.g. --circle_identifier 'circle_map_realign,unicycler'.

required
type: string

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string

Path to FASTA genome file.

type: string
pattern: ^\S+\.fn?a(sta)?(\.gz)?$

Do not load the iGenomes reference config.

hidden
type: boolean

Save the index reference fasta in the results directory.

type: boolean

Path to the directory containg the BWA index files.

type: string

Options to skip various steps within the workflow.

Skip all QC steps except for MultiQC.

type: boolean

Skip MultiQC step.

type: boolean

Skip Picard MarkDuplicates and duplicate filtering

type: boolean

Keep read duplications marked by picard MarkDuplicates.

type: boolean
default: true

Store bam with marked duplicate reads.

type: boolean
default: true

Options to adjust read trimming criteria.

Instructs Trim Galore to remove bp from the 5’ end of read 1 (or single-end reads).

type: integer

Instructs Trim Galore to remove bp from the 5’ end of read 2 (paired-end reads only).

type: integer

Instructs Trim Galore to remove bp from the 3’ end of read 1 AFTER adapter/quality trimming has been performed.

type: integer

Instructs Trim Galore to remove bp from the 3’ end of read 2 AFTER adapter/quality trimming has been performed.

type: integer

Instructs Trim Galore to apply the —nextseq=X option, to trim based on quality after removing poly-G tails.

type: integer

Skip the adapter trimming step.

type: boolean

Save the trimmed FastQ files in the results directory.

type: boolean

Save the merged FastQ files in the results directory.

type: boolean

Parameters used to run Circle-Map.

Store bam file with read candidates for circle-map circular dna calling.

type: boolean

Parameters used to run Circle_finder.

Store bed files created during Circle_finder run.

type: boolean

Parameters used to run Unicycler.

Store fastq intermediate files created during Uniycler run.

type: boolean

parameters used to run ampliconarchitect. The software needs additional data files not included in

Absolute path to the downloaded AA data repository. See AmpliconArchitect.

type: string

Copy Number Threshold for seeds to be considered by AmpliconArchitect.

type: string
default: 4.5

Path to the directory containing the mosek license file ‘mosek.lic’.

type: string

When running AmpliconArchitect, specify reference build [‘GRCh37’, ‘GRCh38’, ‘mm10’]. This is mandatory to match fasta and AA reference build!

type: string

Path to cnn file inside the AmpliconArchitect Data Repository of the respective reference genome. By default it uses the ‘aa_data_repo’ and the ‘reference_build’ input to construct the file path.

type: string

Parameters used to describe centralised config profiles. These should not be edited.

Git commit id for Institutional configs.

hidden
type: string
default: master

Base directory for Institutional configs.

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/configs/master

Institutional config name.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

Set the top limit for requested resources for any single job.

Maximum number of CPUs that can be requested for any single job.

hidden
type: integer
default: 16

Maximum amount of memory that can be requested for any single job.

hidden
type: string
default: 128.GB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Maximum amount of time that can be requested for any single job.

hidden
type: string
default: 240.h
pattern: ^(\d+\.?\s*(s|m|h|d|day)\s*)+$

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

Display help text.

hidden
type: boolean

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

Email address for completion summary, only when pipeline fails.

hidden
type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Send plain-text email instead of HTML.

hidden
type: boolean

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string

Custom config file to supply to MultiQC.

hidden
type: string

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

hidden
type: string

Custom MultiQC yaml file containing HTML including a methods description.

type: string

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

Validation of parameters in lenient more.

hidden
type: boolean