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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringFasta file of primers sequences
stringThe provided file must contains all primers sequences used for sequencing. Gziped files are accepted.
Genome annotation file
stringProvide a GTF annotation file (sorted by sequence and start) if you set the --aligner option to uLTRA
Gziped files are accepted.
Run complete pipeline or TAMA only?
stringIf you don't have the subreads sequences, because of the provider or last PacBio sequencer or because you used Oxford Nanopore, you'll to run the pipeline from the mapping step to advantage of the TAMA processing. This option allows you to change the entry point from subread (--entrypoint isoseq) processing to mapping (--entrypoint map).
If entrypoint 'isoseq', ccs --chunk option, define the number of batches to run in parallel. If entrypoint 'map', split fasta in files of 'chunk' sequences.
integer40If selected entrypoint is 'isoseq' (default): CCS workload can be split into to chunks for a faster running time. This value must be a positive integer greater than 1.
--chunk 1/10
if selected entrypoint is 'map': the reads files will be split into files of 'chunk' sequences.
Email address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
stringUse these options to set CCS parameters
ccs --rq option, define the minimum read quality for CCS selection
number0.9Minimum read quality for a consensus. Under this threshold the sequence is discarded. This value must be in range [0-1].
--rq 0.9
ccs --min-passes option, define the minimum number of passes to select a CCS
integer3Minimum number of full-length subreads required to generate CCS for a ZMW.
ccs --min-snr option, minimum SNR of subreads to use for generating CCS
number2.5Minimum SNR of subreads to use for generating CCS
ccs --min-length option, minimum CCS length for CCS selection
integer10Minimum draft length before polishing
ccs --max-length option, maximum CCS length for CCS selection
integer50000Maximum draft length before polishing
ccs --top-passes option, maximum number of passes to use for CCS generation
integer60Pick at maximum the top N passes for each ZMW
Aligner selection
Aligner to use for mapping: minimap2 or ultra
stringThe uLTRA aligner improve detection of small exons but require an annotation in GTF format to run.
If the genome don't have any reference annotation, you have to use minimap2.
Use these options to set TAMA collapse and TAMA merge parameters
TAMA collapse: Capped RNA?
booleanSet this option if the RNAs are capped.
--capped
TAMA collapse: 5 prime wobble threshold
integer100Set the maximum threshold for collapsing 5 prime exon.
--five_prime 100
TAMA collapse: Splice junction / exon wobble threshold
integer10Set the maximum threshold for collapsing spliced exons.
--splice_junction 10
TAMA collapse: 3 prime wobble threshold
integer100Set the maximum threshold for collapsing 3 prime exon.
--three_prime 100
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)?$This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs. Gziped files are accepted.
Do not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Use 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.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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
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.
Base URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/