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.
boolean
Whether the pipeline should skip assembly steps, and only perform quality control of reads and quantification. —transcript_fasta must be provided if True.
boolean
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.
string
Path to fasta file (not compressed) containing a transcriptome assembly. Only needed if --skip_assembly
is True
.
string
Email 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.
string
File in FASTA format containing possible adapters to remove. Accepted formats: *.{fasta,fna,fas,fa}
string
Specify true
to save files that failed to pass trimming thresholds ending in *.fail.fastq.gz
boolean
Specify true to save all merged reads to the a file ending in *.merged.fastq.gz
boolean
Skip the fastp process if true
boolean
Skip FastQC processes if true
boolean
Extra arguements for fastp. For example, --trim_front1 15 --trim_front2 15 --trim_tail1 5 --trim_tail2 5
string
Enable the removal of reads derived from ribosomal RNA using SortMeRNA.
boolean
Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA.
string
${projectDir}/assets/rrna-db-defaults.txt
If this option is specified, intermediate FastQ files containing non-rRNA reads will be saved in the results directory.
boolean
Assemblers to use. Possible options include trinity
, trinity_no_norm
(trinity without normalized reads), and rnaspades
.
string
trinity,rnaspades
Extra arguments to pass to Trinity command in addition to defaults. Applies to both trinity and trinity_no_norm.
string
Include hard filtered transcripts (in addition to medium filtered transcripts) from rnaSPAdes in the input to EvidentialGene tr2aacds.
boolean
Include soft filtered transcripts (in addition to the medium filtered transcripts) from rnaSPAdes in the input to EvidentialGene tr2aacds.
boolean
Set strand-specific type for rnaSPAdes. Use rf
when first read in pair corresponds to reverse gene strand (antisense data, e.g. obtained via dUTP protocol) and fr
otherwise (forward).
string
Extra arguments for tr2aacds.pl. For example, ‘-MINAA=20’
string
The mode to run BUSCO in. One of genome, proteins, or transcriptome
string
The BUSCO lineage to use, or auto
to automatically select lineage
string
auto
Path to local BUSCO lineages directory.
string
Path to BUSCO config file.
string
Path to FASTA genome file.
string
^\S+\.fn?a(sta)?(\.gz)?$
File with gene coordinates in GTF/GFF format (needs information about parent relations). rnaQUAST authors recommend to use files downloaded from GENCODE or Ensembl.
string
Path to FASTA file of reference set of proteins or transcripts from a related species
string
Override library type inferred based on strandedness defined in meta object. A
for auto.
string
A
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Less common options for the pipeline, typically set in a config file.
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
Email 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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Base URL or local path to location of pipeline test dataset files
string
https://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
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
Directory / URL base for iGenomes references.
string
s3://ngi-igenomes/igenomes/
Do not load the iGenomes reference config.
boolean