nf-core/isoseq
Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.
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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringFasta file of primers sequences
stringGenome annotation file
stringRun complete pipeline or TAMA only?
stringIf entrypoint ‘isoseq’, ccs —chunk option, define the number of batches to run in parallel. If entrypoint ‘map’, split fasta in files of ‘chunk’ sequences.
integer40Email address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringUse these options to set CCS parameters
ccs —rq option, define the minimum read quality for CCS selection
number0.9ccs —min-passes option, define the minimum number of passes to select a CCS
integer3ccs —min-snr option, minimum SNR of subreads to use for generating CCS
number2.5ccs —min-length option, minimum CCS length for CCS selection
integer10ccs —max-length option, maximum CCS length for CCS selection
integer50000ccs —top-passes option, maximum number of passes to use for CCS generation
integer60Aligner selection
Aligner to use for mapping: minimap2 or ultra
stringUse these options to set TAMA collapse and TAMA merge parameters
TAMA collapse: Capped RNA?
booleanTAMA collapse: 5 prime wobble threshold
integer100TAMA collapse: Splice junction / exon wobble threshold
integer10TAMA collapse: 3 prime wobble threshold
integer100TAMA merge: merge the sample-wise annotations into a single annotation?
booleanOptions to skip various steps within the workflow.
Skip lima
booleanReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Do not load the iGenomes reference config.
booleanThe base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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