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)$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringSpecify which tools RNAvar should use for annotating variants. Values can be ‘snpeff’, ‘vep’ or ‘merge’. If you specify ‘merge’, the pipeline runs both snpeff and VEP annotation.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringSave FastQ files after merging re-sequenced libraries in the results directory.
booleanReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath 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
number150If generated by the pipeline, save the STAR index in the results directory.
booleanPath to known indels VCF file(s)
stringPath to known indels index file(s)
stringPath to dbSNP VCF file
stringPath to dbSNP VCF index file
stringsnpEff DB version.
stringVEP genome.
stringVEP species.
stringVEP cache version.
integer,stringType of feature to parse from annotation file
stringDownload annotation cache.
booleanDo not load the iGenomes reference config.
booleanThe base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Parameters for postprocessing of alignment files.
Specify whether to remove duplicates from the BAM during Picard MarkDuplicates step.
booleanDefine parameters related to read alignment
Specifies the alignment algorithm to use.
stringPath to STAR index folder or compressed file (tar.gz)
stringEnable STAR 2-pass mapping mode.
booleanDo not use GTF file during STAR index building step
booleanOption to limit RAM when sorting BAM file. Value to be specified in bytes. If 0, will be set to the genome index size.
integerSpecifies the number of genome bins for coordinate-sorting
integer50Specifies the maximum number of collapsed junctions
integer1000000Specifies the maximum intron size
integerSequencing center information to be added to read group of BAM files.
stringSpecify the sequencing platform used
stringilluminaWhere possible, save unaligned reads from aligner to the results directory.
booleanSave the intermediate BAM files from the alignment step.
booleanCreate a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes.
booleanParameters for preprocessing FASTQ files before alignment.
Specify whether to remove UMIs from the reads with UMI-tools extract.
booleanUMI pattern to use. Can be either ‘string’ (default) or ‘regex’.
stringThe 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.
stringParameters for variant calling tools.
The minimum phred-scaled confidence threshold at which variants should be called.
integer20Enable generation of GVCFs by sample additionnaly to the VCFs.
booleanParameters for variant annotation tools.
Path to VEP cache.
strings3://annotation-cache/vep_cache/Path to snpEff cache.
strings3://annotation-cache/snpeff_cache/Allow usage of fasta file for annotation with VEP
booleanEnable the use of the VEP dbNSFP plugin.
booleanPath to dbNSFP processed file.
string^\S+\.gz$Path to dbNSFP tabix indexed file.
string^\S+\.tbi$Consequence to annotate with
stringFields to annotate with
stringrs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AFEnable the use of the VEP LOFTEE plugin.
booleanEnable the use of the VEP SpliceAI plugin.
booleanPath 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.
booleanAdd an extra custom argument to VEP.
string--everything --filter_common --per_gene --total_length --offline --format vcfUse annotation cache keys for snpeff_cache and vep_cache. Only when using annotation-cache or a similar structure. See here for more information.
booleanThe output directory where the cache will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringVEP output-file format.
stringDefine parameters that control the stages in the pipeline
Skip the process of base recalibration steps i.e., GATK BaseRecalibrator and GATK ApplyBQSR.
booleanSkip the process of preparing interval lists for the GATK variant calling step
booleanSkip variant filtering of GATK
booleanSkip variant annotation
booleanSkip MultiQC reports
booleanSkip the check of the exon bed
booleanDefine 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
integer25Do not use gene interval file during variant calling
booleanThe window size (in bases) in which to evaluate clustered SNPs.
integer35The number of SNPs which make up a cluster. Must be at least 2.
integer3Value to be used for the FisherStrand (FS) filter
number30Value to be used for the QualByDepth (QD) filter
number2Parameters 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/modules/data/Base URL or local path to location of pipeline test dataset files
stringhttps://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