Params

A Nextflow pipeline for base NGS analysis.

Input/output options

Parameter	Description	Type	Default	Required
`projectTitle`	A short title for the project. Used in naming files/directories.	`string`		True
`samplesheet`	Path to input samplesheet in CSV format.	`string`		True
`genome`	A path or URL to the reference genome sequence file in fasta format. Help For reasons of reproducibility and portability we recommend using direct links to reference genome sequence files available through repositories such as RefSeq and Ensembl.	`string`		True
`annotations`	A path or URL to the reference genome annotations file in GTF format. Help For reasons of reproducibility and portability we recommend using direct links to reference annotation files available through repositories such as RefSeq and Ensembl.	`string`		True
`publishDirData`	Base directory in which output data files will be published. Help We think of this pipeline as producing as producing two main types of output: data and reports. Data files are raw or processed files that are used for generating results and insights. They typically are not immediately interpretable by humans and often are not even human readable. Examples of data files would include raw fastq files, mappings in BAM format, tables of read counts within genes.	`string`	${launchDir}/data
`publishDirReports`	Base directory in which output reports files will be published. Help We think of this pipeline as producing as producing two main types of output: data and reports. Reports files are processed files that are used for immediately producing insights. They typically immediately interpretable by humans. Examples of reports files would include MultiQC reports and MultiQC data tables, summary statistics files produced by Samtools stats, etc.	`string`	${launchDir}/reports
`publishMode`	Method for publishing files. Help This sets the default mode for publishing files. See the `mode` section of the `publishDir` Nextflow docs for details about the options.	`string`	copy
`exploratoryTag`	Tag to add to the end of the exploratory directory name to describe what's being explored. Use in conjunction with the `exploratory` profile.	`string`

Read trim/filter options

Parameter	Description	Type	Default	Required	Hidden
`trimTool`	Tool for read trimming/filtering.	`string`	fastp	True
`adapterFasta`	Fasta file of adapters for read trimming. Help `cutadapt` does not currently work with an adapter fasta file.	`string`	${projectDir}/assets/NO_FILE

Mapping parameters

Parameter	Description	Type	Default	Required	Hidden
`mapTool`	Tool for mapping reads.	`string`	bwamem2	True

Skip steps options

Options to skip pipeline execution steps.

Parameter	Description	Type
`skipTrimReads`	Skip read trimming steps. Will use raw reads for all downstream steps, e.g. read mapping.	`boolean`
`skipRawReadDepth`	Skip computing read depth for raw reads.	`boolean`
`skipPrealignReadDepth`	Skip computing read depth for prealign reads.	`boolean`