nf-core/rnavar
gatk4 RNA variant calling pipeline
1.0.0). The latest
stable release is
1.1.0
.
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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
stringPath to FASTA reference index.
stringDirectory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
booleanPath to GTF annotation file.
stringPath to GFF3 annotation file.
stringPath to BED file containing exon intervals. This will be created from the GTF file if not specified.
stringRead length
number151If generated by the pipeline, save the STAR index in the results directory.
booleanPath to known indels VCF file
stringPath to known indels index file
stringPath to dbSNP VCF file
stringPath to dbSNP VCF index file
stringsnpEff DB version
stringVEP genome
stringVEP species
stringVEP cache version
stringDefine parameters related to read alignment
Specifies the alignment algorithm to use. Currently available option is ‘star’
stringstarPath to STAR index folder or compressed file (tar.gz)
stringEnable STAR 2-pass mapping mode.
booleanDo not use GTF file during STAR index buidling 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
integer1000000Sequencing 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.
booleanSpecify whether to remove duplicates from the BAM during Picard MarkDuplicates step.
booleanThe minimum phred-scaled confidence threshold at which variants should be called.
number20Specify 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.
stringEnable the use of cache for annotation
booleanEnable CADD cache.
booleanPath to CADD InDels file.
stringPath to CADD InDels index.
stringPath to CADD SNVs file.
stringPath to CADD SNVs index.
stringEnable the use of the VEP GeneSplicer plugin.
booleanPath to snpEff cache
stringPath to VEP cache
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
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.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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$Do not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanRun this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
boolean