nf-core/rnavar
gatk4 RNA variant calling pipeline
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|tsv|yaml|yml|json)$
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Specify which tools RNAvar should use for annotating variants. Values can be ‘snpeff’, ‘vep’ or ‘merge’. If you specify ‘merge’, the pipeline runs both snpeff and VEP annotation.
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
Save FastQ files after merging re-sequenced libraries in the results directory.
boolean
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
Path to FASTA genome file.
string
^\S+\.fn?a(sta)?(\.gz)?$
Path to FASTA dictionary file.
string
^\S+\.dict$
Path to FASTA reference index.
string
^\S+\.fai$
Path to GTF annotation file.
string
^\S+\.gtf$
Path to GFF3 annotation file.
string
^\S+\.gff\d?$
Path to BED file containing exon intervals. This will be created from the GTF file if not specified.
string
^\S+\.bed$
Read length
number
150
If generated by the pipeline, save the STAR index in the results directory.
boolean
Path to known indels VCF file(s)
string
Path to known indels index file(s)
string
Path to dbSNP VCF file
string
Path to dbSNP VCF index file
string
snpEff DB version.
string
VEP genome.
string
VEP species.
string
VEP cache version.
integer,string
Type of feature to parse from annotation file
string
Download annotation cache.
boolean
Do not load the iGenomes reference config.
boolean
The base path to the igenomes reference files
string
s3://ngi-igenomes/igenomes/
Parameters for postprocessing of alignment files.
Specify whether to remove duplicates from the BAM during Picard MarkDuplicates step.
boolean
Define parameters related to read alignment
Specifies the alignment algorithm to use.
string
Path to STAR index folder or compressed file (tar.gz)
string
Enable STAR 2-pass mapping mode.
boolean
Do not use GTF file during STAR index building step
boolean
Option to limit RAM when sorting BAM file. Value to be specified in bytes. If 0, will be set to the genome index size.
integer
Specifies the number of genome bins for coordinate-sorting
integer
50
Specifies the maximum number of collapsed junctions
integer
1000000
Specifies the maximum intron size
integer
Sequencing center information to be added to read group of BAM files.
string
Specify the sequencing platform used
string
illumina
Where possible, save unaligned reads from aligner to the results directory.
boolean
Save the intermediate BAM files from the alignment step.
boolean
Create a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes.
boolean
Parameters for preprocessing FASTQ files before alignment.
Specify whether to remove UMIs from the reads with UMI-tools extract.
boolean
UMI pattern to use. Can be either ‘string’ (default) or ‘regex’.
string
The UMI barcode pattern to use e.g. ‘NNNNNN’ indicates that the first 6 nucleotides of the read are from the UMI.
string
^[NXC]*$
The UMI barcode pattern to use if the UMI is located in read 2.
string
^[NXC]*$
The character that separates the UMI in the read name. Most likely a colon if you skipped the extraction with UMI-tools and used other software.
string
Parameters for variant calling tools.
The minimum phred-scaled confidence threshold at which variants should be called.
integer
20
Enable generation of GVCFs by sample additionnaly to the VCFs.
boolean
Parameters for variant annotation tools.
Path to VEP cache.
string
s3://annotation-cache/vep_cache/
Path to snpEff cache.
string
s3://annotation-cache/snpeff_cache/
Allow usage of fasta file for annotation with VEP
boolean
Enable the use of the VEP dbNSFP plugin.
boolean
Path to dbNSFP processed file.
string
^\S+\.gz$
Path to dbNSFP tabix indexed file.
string
^\S+\.tbi$
Consequence to annotate with
string
Fields to annotate with
string
rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF
Enable the use of the VEP LOFTEE plugin.
boolean
Enable the use of the VEP SpliceAI plugin.
boolean
Path to spliceai raw scores snv file.
string
^\S+\.vcf\.gz$
Path to spliceai raw scores snv tabix indexed file.
string
^\S+\.tbi$
Path to spliceai raw scores indel file.
string
^\S+\.vcf\.gz$
Path to spliceai raw scores indel tabix indexed file.
string
^\S+\.tbi$
Enable the use of the VEP SpliceRegion plugin.
boolean
Add an extra custom argument to VEP.
string
--everything --filter_common --per_gene --total_length --offline --format vcf
Use annotation cache keys for snpeff_cache and vep_cache. Only when using annotation-cache or a similar structure. See here for more information.
boolean
The output directory where the cache will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
VEP output-file format.
string
Define parameters that control the stages in the pipeline
Skip the process of base recalibration steps i.e., GATK BaseRecalibrator and GATK ApplyBQSR.
boolean
Skip the process of preparing interval lists for the GATK variant calling step
boolean
Skip variant filtering of GATK
boolean
Skip variant annotation
boolean
Skip MultiQC reports
boolean
Skip the check of the exon bed
boolean
Define parameters of the tools used in the pipeline
Number of times the gene interval list to be split in order to run GATK haplotype caller in parallel
integer
25
Do not use gene interval file during variant calling
boolean
The window size (in bases) in which to evaluate clustered SNPs.
integer
35
The number of SNPs which make up a cluster. Must be at least 2.
integer
3
Value to be used for the FisherStrand (FS) filter
number
30
Value to be used for the QualByDepth (QD) filter
number
2
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/modules/data/
Base URL or local path to location of pipeline test dataset files
string
https://raw.githubusercontent.com/nf-core/test-datasets/rnavar/data/
Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string