nf-core/denovotranscript
A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq
Whether the pipeline should only perform quality control, and skip assembly and quantification.
booleanWhether the pipeline should skip assembly steps, and only perform quality control of reads and quantification. --transcript_fasta must be provided if True.
booleanDefine 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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringPath to fasta file (not compressed) containing a transcriptome assembly. Only needed if --skip_assembly is True.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
stringFile in FASTA format containing possible adapters to remove. Accepted formats: *.{fasta,fna,fas,fa}
stringSpecify true to save files that failed to pass trimming thresholds ending in *.fail.fastq.gz
booleanSpecify true to save all merged reads to the a file ending in *.merged.fastq.gz
booleanSkip the fastp process if true
booleanSkip FastQC processes if true
booleanExtra arguements for fastp. For example, --trim_front1 15 --trim_front2 15 --trim_tail1 5 --trim_tail2 5{:bash}
stringEnable the removal of reads derived from ribosomal RNA using SortMeRNA.
booleanText file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA.
string${projectDir}/assets/rrna-db-defaults.txtIf this option is specified, intermediate FastQ files containing non-rRNA reads will be saved in the results directory.
booleanAssemblers to use. Possible options include trinity, trinity_no_norm (trinity without normalized reads), and rnaspades.
stringtrinity,rnaspadesExtra arguments to pass to Trinity command in addition to defaults. Applies to both trinity and trinity_no_norm.
stringInclude hard filtered transcripts (in addition to medium filtered transcripts) from rnaSPAdes in the input to EvidentialGene tr2aacds.
booleanInclude soft filtered transcripts (in addition to the medium filtered transcripts) from rnaSPAdes in the input to EvidentialGene tr2aacds.
booleanSet strand-specific type for rnaSPAdes. Use --ss rf when first read in pair corresponds to reverse gene strand (antisense data, e.g. obtained via dUTP protocol) and --ss fr otherwise (forward).
stringNote, that strand-specificity is not related and should not be confused with FR and RF orientation of paired reads. RNA-Seq paired-end reads typically have forward-reverse orientation (--> <--), which is assumed by default and no additional options are needed.
Extra arguments for tr2aacds.pl. For example, '-MINAA=20'
stringThe mode to run BUSCO in. One of genome, proteins, or transcriptome
stringThe BUSCO lineage to use, or auto to automatically select lineage
stringautoPath to local BUSCO lineages directory.
stringPath to BUSCO config file.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$This parameter can be used to provide a reference to rnaQUAST.
File with gene coordinates in GTF/GFF format (needs information about parent relations). rnaQUAST authors recommend to use files downloaded from GENCODE or Ensembl.
stringPath to FASTA file of reference set of proteins or transcripts from a related species
stringOverride library type inferred based on strandedness defined in meta object. A for auto.
stringAParameters 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/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.
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.