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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringPath to fasta file (not compressed) containing a transcriptome assembly. Only needed if --skip_assembly is True.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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
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${projectDir}/assets/rrna-db-defaults.txtIf this option is specified, intermediate FastQ files containing non-rRNA reads will be saved in the results directory.
booleanAssemblers to use. Possible options include trinity, trinity_no_norm (trinity without normalized reads), and rnaspades.
stringtrinity,rnaspadesExtra arguments to pass to Trinity command in addition to defaults. Applies to both trinity and trinity_no_norm.
stringInclude hard filtered transcripts (in addition to medium filtered transcripts) from rnaSPAdes in the input to EvidentialGene tr2aacds.
booleanInclude soft filtered transcripts (in addition to the medium filtered transcripts) from rnaSPAdes in the input to EvidentialGene tr2aacds.
booleanSet strand-specific type for rnaSPAdes. Use rf when first read in pair corresponds to reverse gene strand (antisense data, e.g. obtained via dUTP protocol) and fr otherwise (forward).
stringExtra arguments for tr2aacds.pl. For example, ‘-MINAA=20’
stringThe mode to run BUSCO in. One of genome, proteins, or transcriptome
stringThe BUSCO lineage to use, or auto to automatically select lineage
stringautoPath to local BUSCO lineages directory.
stringPath to BUSCO config file.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$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/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.
stringReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringDirectory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/Do not load the iGenomes reference config.
boolean