dalmolingroup/bulkrna pipeline parameters

Workflow for pre-processing, alignment and quantification of bulk RNA-Seq data

Input/output options

Define where the pipeline should find input data and save output data.

Parameter	Description	Type
`input`	Path to comma-separated file containing information about the samples in the experiment. Help 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.	`string`
`outdir`	The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.	`string`
`email`	Email address for completion summary. Help 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.	`string`
`multiqc_title`	MultiQC report title. Printed as page header, used for filename if not otherwise specified.	`string`

FastP trimming options

Define fastp parameters for trimming

Parameter	Description	Type	Default
`reads_minlength`	reads shorter than length_required will be discarded	`integer`	15
`fastp_adapter_fasta`	specify a FASTA file to trim both read1 and read2 (if PE) by all the sequences in this FASTA file	`string`	https://gist.githubusercontent.com/jvfe/2d569adf47791b9d1e1b4ff810d410b8/raw/e970485d7fe2c9a5b501966eb26e9eb51789c86d/sample_adapters.fa
`fastp_save_trimmed_fail`	save reads that cannot pass the filters	`boolean`
`fastp_save_merged`	for paired-end input, merge each pair of reads into a single read if they are overlapped	`boolean`
`fastp_qualified_quality`	the quality value that a base is qualified	`integer`	15
`fastp_cut_mean_quality`	the mean quality requirement option shared by the cut_front and cut_tail sliding windows	`integer`	15

Kallisto options

Options for the alignment/quantification

Parameter	Description	Type	Default
`transcriptome`	Path to the transcriptome FASTA file to use for reference	`string`	None
`index`		`string`	None
`fragment_length`	Estimated average fragment length	`integer`	100
`fragment_length_sd`	Estimated standard deviation of fragment length	`integer`	1

TXimport options

Options for importing Kallisto results into a count matrix

Parameter	Description	Type	Default
`gtf`		`string`	None

Institutional config options

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

Parameter	Description	Type	Default
`custom_config_version`	Git commit id for Institutional configs.	`string`	master
`custom_config_base`	Base directory for Institutional configs. Help If 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.	`string`	https://raw.githubusercontent.com/nf-core/configs/master
`config_profile_name`	Institutional config name.	`string`
`config_profile_description`	Institutional config description.	`string`
`config_profile_contact`	Institutional config contact information.	`string`
`config_profile_url`	Institutional config URL link.	`string`

Max job request options

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

Parameter	Description	Type	Default
`max_cpus`	Maximum number of CPUs that can be requested for any single job. Help Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`	`integer`	16
`max_memory`	Maximum amount of memory that can be requested for any single job. Help 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'`	`string`	128.GB
`max_time`	Maximum amount of time that can be requested for any single job. Help 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'`	`string`	240.h

Generic options

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

Parameter	Description	Type	Default
`help`	Display help text.	`boolean`
`publish_dir_mode`	Method used to save pipeline results to output directory. Help The 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.	`string`	copy
`email_on_fail`	Email address for completion summary, only when pipeline fails. Help An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.	`string`
`plaintext_email`	Send plain-text email instead of HTML.	`boolean`
`max_multiqc_email_size`	File size limit when attaching MultiQC reports to summary emails.	`string`	25.MB
`monochrome_logs`	Do not use coloured log outputs.	`boolean`
`hook_url`	Incoming hook URL for messaging service Help Incoming hook URL for messaging service. Currently, only MS Teams is supported.	`string`
`multiqc_config`	Custom config file to supply to MultiQC.	`string`
`multiqc_logo`	Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file	`string`
`multiqc_methods_description`	Custom MultiQC yaml file containing HTML including a methods description.	`string`
`tracedir`	Directory to keep pipeline Nextflow logs and reports.	`string`	${params.outdir}/pipeline_info
`validate_params`	Boolean whether to validate parameters against the schema at runtime	`boolean`	True
`show_hidden_params`	Show all params when using `--help` Help By 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.	`boolean`