nf-core/nascent
Nascent Transcription Processing Pipeline
2.1.1). The latest
stable release is
2.3.0
.
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.
stringSkip groHMM tuning step as it can take a long time.
booleanSkip groHMM all together
booleanFile of parameters to test for groHMM tuning
string^\S+\.csv$Undesired regions, that transcripts should not overlap with
string^\S+\.bed(\.gz)?$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)?$Path to GFF3 annotation file.
string^\S+\.gff(\.gz)?$Path to BED file containing gene intervals. This will be created from the GTF file if not specified.
string^\S+\.bed(\.gz)?$Path to BWA mem indices.
stringPath to bwa-mem2 mem indices.
stringPath to dragmap indices.
stringIf generated by the pipeline save the BWA index in the results directory.
booleanDirectory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
booleanParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
boolean