nf-core/nascent
Nascent Transcription Processing Pipeline
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.
stringSpecify aligner to be used to map reads to reference genome.
stringSkip all of the alignment-based processes within the pipeline.
booleanSkip the adapter trimming step.
booleanUse this if your input FastQ files have already been trimmed outside of the workflow or if you're very confident that there is no adapter contamination in your data.
Options for processing reads with unique molecular identifiers
Enable UMI-based read deduplication.
booleanGenerate output stats when running "umi_tools dedup".
booleanIt can be quite time consuming generating these output stats - see #827.
Type of experiment to use for Transcript Identification(NT or TSS)
What type of nascent or TSS assay the sample is.
stringUse HOMER uniqmap for transcript identification.
booleanEnable this to use HOMER's uniqmap functionality for more accurate transcript identification in repetitive regions.
Skip groHMM all together
booleanMinimum number of UTs to use for groHMM.
integer5Maximum number of UTs to use for groHMM.
integer45Minimum LTProbB value to use for groHMM.
integer-100Depends on how you look at this one, which is the minimum and maximum... But I figured most will ignore the negative, so we went with absolute values.
Maximum LTProbB value to use for groHMM.
integer-400Depends on how you look at this one, which is the minimum and maximum... But I figured most will ignore the negative, so we went with absolute values.
Undesired regions, that transcripts should not overlap with
string^\S+\.bed(\.gz)?$Promoter regions, or gene regions are a good example
Desired regions, that transcripts should overlap with
string^\S+\.bed(\.gz)?$Histone Modifications(H3K4me1 and H3K27ac), or known TREs from the PINTS element matrix are examples
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)?$This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
Path to GTF annotation file.
string^\S+\.gtf(\.gz)?$This parameter is mandatory if --genome is not specified.
Path to GFF3 annotation file.
string^\S+\.gff(3)?(\.gz)?$This parameter must be specified if --genome or --gtf are not specified.
Path to BED file containing gene intervals. This will be created from the GTF file if not specified.
string^\S+\.bed(\.gz)?$Path to BWA mem indices.
stringNB If none provided, will be generated automatically from the FASTA reference.
Path to bwa-mem2 mem indices.
stringNB If none provided, will be generated automatically from the FASTA reference.
Path to dragmap indices.
stringIf you use AWS iGenomes, this has already been set for you appropriately.
If you wish to recompute indices available on igenomes, set --dragmap false.
NB If none provided, will be generated automatically from the FASTA reference, if
--aligner dragmapis specified. Combine with--save_referenceto save for future runs.
Path to bowtie2 indices.
stringIf you use AWS iGenomes, this has already been set for you appropriately.
If you wish to recompute indices available on igenomes, set --dragmap false.
NB If none provided, will be generated automatically from the FASTA reference, if
--aligner bowtie2is specified. Combine with--save_referenceto save for future runs.
Path to HISAT2 indices.
stringNB If none provided, index will NOT be generated automatically from the FASTA reference. See nf-core/references if a custom index is needed.
Path to STAR indices.
stringNB If none provided, index will be generated automatically from the FASTA reference.
Path to HOMER uniqmap file or URL to download.
stringNB If none provided, will be downloaded automatically from the HOMER website. See nf-core/references for generation
If generated by the pipeline save the BWA 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.
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.
The base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Directory / URL base for CHM13 references.
stringhttps://s3-us-west-2.amazonaws.com/human-pangenomicsParameters 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.
stringLess common options for the pipeline, typically set in a config file.
Display 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.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/