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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
booleanOptions for processing reads with unique molecular identifiers
Enable UMI-based read deduplication.
booleanGenerate output stats when running “umi_tools dedup”.
booleanType 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.
booleanSkip 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-100Maximum LTProbB value to use for groHMM.
integer-400Undesired regions, that transcripts should not overlap with
string^\S+\.bed(\.gz)?$Desired regions, that transcripts should overlap with
string^\S+\.bed(\.gz)?$Reference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Path to GTF annotation file.
string^\S+\.gtf(\.gz)?$Path to GFF3 annotation file.
string^\S+\.gff(3)?(\.gz)?$Path to BED file containing gene intervals. This will be created from the GTF file if not specified.
string^\S+\.bed(\.gz)?$Path to BWA mem indices.
stringPath to bwa-mem2 mem indices.
stringPath to dragmap indices.
stringPath to bowtie2 indices.
stringPath to HISAT2 indices.
stringPath to STAR indices.
stringPath to HOMER uniqmap file or URL to download.
stringIf generated by the pipeline save the BWA index in the results directory.
booleanDo not load the iGenomes reference config.
booleanThe 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/masterInstitutional 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.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom 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/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string