nf-core/riboseq
Pipeline for the analysis of ribosome profiling, or Ribo-Seq (also named ribosome footprinting) 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.
stringYou 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.
stringSet 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.
stringReference 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.
stringThis 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.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo 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.
Path to FASTA genome file.
stringPath to FASTA transcriptome file.
stringPath to gtf files
stringSplice sites file required for HISAT2.
stringPath to FASTA rRNA file.
stringPath to directory containing index rRNA files from riboviz pipeline.
stringBuilding indexes for alignement.
booleantrueadapter sequence trimming required in the workflow.
undefinedAGATCGGAAGAGCACACGTCTGAAbooleanOptions for processing reads with unique molecular identifiers
Enable UMI-based read deduplication.
booleanUMI pattern to use. Can be either 'string' (default) or 'regex'.
stringstringMore details can be found in the UMI-tools documentation.
Skip the UMI extraction from the read in case the UMIs have been moved to the headers in advance of the pipeline run.
booleanRegular expression pattern for UMI extraction
string.*(?P<umi_1>.{5})(?P<discard_1>.{5})$The regular expression pattern used to extract UMIs from the reads. The pattern must include 'Ns' for the UMIs (Unique Molecular Identifiers) and can optionally include 'Bs' for the barcodes used for demultiplexing. The value of umi_regexp is expected to be a string that represents this pattern.
Generate output stats when running "umi_tools dedup".
booleanIt can be quite time consuming generating these output stats - see #827.
Aligning the fastq files to transcriptome and rRNA.
Specifies the alignment algorithm to use - available options are 'star_salmon', 'star_rsem' and 'hisat2'.
stringSkip all of the alignment-based processes within the pipeline.
booleanSequencing center information to be added to read group of BAM files.
stringWhere possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory.
booleanThis may either be in the form of FastQ or BAM files depending on the options available for that particular tool.
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.GBUse 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.hUse 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.
stringAn 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.MBDo 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.
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.