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$A design file with information about the samples in your experiment. Use this parameter to specify the location of the input files. It has to be a comma-separated file with a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
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.
stringIf using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.
See the nf-core website docs for more details.
Path to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
Path to FASTA dictionary file.
stringNB If none provided, will be generated automatically from the FASTA reference.
Path to FASTA reference index.
stringNB If none provided, will be generated automatically from the FASTA reference
Path to GTF annotation file.
stringThis parameter is mandatory if --genome is not specified.
Path to GFF3 annotation file.
stringThis parameter must be specified if --genome or --gtf are not specified.
Path to BED file containing exon intervals. This will be created from the GTF file if not specified.
stringRead length
number150Specify the read length for the STAR aligner.
If generated by the pipeline, save the STAR index in the results directory.
booleanIf the STAR index is generated by the pipeline, then please use this parameter to save it to your results folder. These index can then be used for future pipeline runs, reducing processing times.
Path 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.
stringIf you use AWS iGenomes, this has already been set for you appropriately.
This is used to specify the database to be use to annotate with.
Alternatively databases' names can be listed with the snpEff databases.
snpEff genome.
stringIf you use AWS iGenomes, this has already been set for you appropriately.
This is used to specify the genome when using the container with pre-downloaded cache.
VEP genome.
stringIf you use AWS iGenomes, this has already been set for you appropriately.
This is used to specify the genome when using the container with pre-downloaded cache.
VEP species.
stringIf you use AWS iGenomes, this has already been set for you appropriately.
Alternatively species listed in Ensembl Genomes caches can be used.
VEP cache version.
numberIf you use AWS iGenomes, this has already been set for you appropriately.
Alternatively cache version can be use to specify the correct Ensembl Genomes version number as these differ from the concurrent Ensembl/VEP version numbers
Type of feature to parse from annotation file
stringThis parameter value can be exon, transcript or gene. Default exon
Download annotation cache.
booleanSet this parameter, if you wish to download annotation cache.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/Do not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
Define parameters related to read alignment
Specifies the alignment algorithm to use. Currently available option is 'star'
stringstarThis parameter define which aligner is to be used for aligning the RNA reads to the reference genome. Currently only STAR aligner is supported. So use 'star' as the value for this option.
Path to STAR index folder or compressed file (tar.gz)
stringThis parameter can be used if there is an pre-defined STAR index available. You can either give the full path to the index directory or a compressed file in tar.gz format.
Enable STAR 2-pass mapping mode.
booleanThis parameter enables STAR to perform 2-pass mapping. Default true.
Do not use GTF file during STAR index buidling step
booleanDo not use parameter --sjdbGTFfile <GTF file> during the STAR genomeGenerate process.
Option to limit RAM when sorting BAM file. Value to be specified in bytes. If 0, will be set to the genome index size.
integerThis parameter specifies the maximum available RAM (bytes) for sorting BAM during STAR alignment.
Specifies the number of genome bins for coordinate-sorting
integer50This parameter specifies the number of bins to be used for coordinate sorting during STAR alignment step.
Specifies the maximum number of collapsed junctions
integer1000000Sequencing center information to be added to read group of BAM files.
stringThis parameter is required for creating a proper BAM header to use in the downstream analysis of GATK.
Specify the sequencing platform used
stringilluminaThis parameter is required for creating a proper BAM header to use in the downstream analysis of GATK.
Where possible, save unaligned reads from aligner to the results directory.
booleanThis may either be in the form of FastQ or BAM files depending on the options available for that particular tool.
Save the intermediate BAM files from the alignment step.
booleanBy default, intermediate BAM files will not be saved. The final BAM files created after the appropriate filtering step are always saved to limit storage usage. Set this parameter to also save other intermediate BAM files.
Create 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.
booleanSpecify true for removing duplicates from BAM file during Picard MarkDuplicates step.
The minimum phred-scaled confidence threshold at which variants should be called.
number20Specify the minimum phred-scaled confidence threshold at which variants should be called.
Enable generation of GVCFs by sample additionnaly to the VCFs.
booleanThis parameter enables GATK HAPLOTYPECALLER to generate GVCFs. Default false.
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.
stringList of tools to be used for variant annotation.
This parameter must be a combination of the following values:snpeff, vep, mergePath to VEP cache.
strings3://annotation-cache/vep_cache/Path to VEP cache which should contain the relevant species, genome and build directories at the path ${vep_species}/${vep_genome}_${vep_cache_version}
Path to snpEff cache.
strings3://annotation-cache/snpeff_cache/Path to snpEff cache which should contain the relevant genome and build directory in the path ${snpeff_species}.${snpeff_version}
Allow usage of fasta file for annotation with VEP
booleanBy pointing VEP to a FASTA file, it is possible to retrieve reference sequence locally. This enables VEP to retrieve HGVS notations (--hgvs), check the reference sequence given in input data, and construct transcript models from a GFF or GTF file without accessing a database.
For details, see here.
Path to dbNSFP processed file.
stringTo be used with --vep_dbnsfp.
dbNSFP files and more information are available at https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#dbnsfp and https://sites.google.com/site/jpopgen/dbNSFP/
Path to dbNSFP tabix indexed file.
stringTo be used with --vep_dbnsfp.
Consequence to annotate with
stringTo be used with --vep_dbnsfp.
This params is used to filter/limit outputs to a specific effect of the variant.
The set of consequence terms is defined by the Sequence Ontology and an overview of those used in VEP can be found here: https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html
If one wants to filter using several consequences, then separate those by using '&' (i.e. 'consequence=3_prime_UTR_variant&intron_variant'.
Fields to annotate with
stringrs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AFTo be used with --vep_dbnsfp.
This params can be used to retrieve individual values from the dbNSFP file. The values correspond to the name of the columns in the dbNSFP file and are separated by comma.
The column names might differ between the different dbNSFP versions. Please check the Readme.txt file, which is provided with the dbNSFP file, to obtain the correct column names. The Readme file contains also a short description of the provided values and the version of the tools used to generate them.
Default value are explained below:
rs_dbSNP - rs number from dbSNP
HGVSc_VEP - HGVS coding variant presentation from VEP. Multiple entries separated by ';', corresponds to Ensembl_transcriptid
HGVSp_VEP - HGVS protein variant presentation from VEP. Multiple entries separated by ';', corresponds to Ensembl_proteinid
1000Gp3_EAS_AF - Alternative allele frequency in the 1000Gp3 East Asian descendent samples
1000Gp3_AMR_AF - Alternative allele counts in the 1000Gp3 American descendent samples
LRT_score - Original LRT two-sided p-value (LRTori), ranges from 0 to 1
GERP++_RS - Conservation score. The larger the score, the more conserved the site, ranges from -12.3 to 6.17
gnomAD_exomes_AF - Alternative allele frequency in the whole gnomAD exome samples.
Path to spliceai raw scores snv file.
stringTo be used with --vep_spliceai.
Path to spliceai raw scores snv tabix indexed file.
stringTo be used with --vep_spliceai.
Path to spliceai raw scores indel file.
stringTo be used with --vep_spliceai.
Path to spliceai raw scores indel tabix indexed file.
stringTo be used with --vep_spliceai.
Add an extra custom argument to VEP.
string--everything --filter_common --per_gene --total_length --offline --format vcfUsing this params you can add custom args to VEP.
Use 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.
stringSets the format of the output-file from VEP. Available formats: json, tab and vcf.
Define parameters that control the stages in the pipeline
Skip the process of base recalibration steps i.e., GATK BaseRecalibrator and GATK ApplyBQSR.
booleanThis parameter disable the base recalibration step, thus using a un-calibrated BAM file for variant calling.
Skip the process of preparing interval lists for the GATK variant calling step
booleanThis parameter disable preparing multiple interval lists to use with HaplotypeCaller module of GATK. It is recommended not to disable the step as it is required to run the variant calling correctly.
Skip variant filtering of GATK
booleanSet this parameter if you don't want to filter any variants.
Skip variant annotation
booleanSet this parameter if you don't want to run variant annotation.
Skip MultiQC reports
booleanThis parameter disable all QC reports
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
integer25Set this parameter to decide the number of splits for the gene interval list file.
Do not use gene interval file during variant calling
booleanThis parameter, if set to True, does not use the gene intervals during the variant calling step, which then results in variants from all regions including non-genic. Default is False
The window size (in bases) in which to evaluate clustered SNPs.
integer35This parameter is used by GATK variant filteration step. It defines the window size (in bases) in which to evaluate clustered SNPs. It has to be used together with the other option 'cluster'.
The number of SNPs which make up a cluster. Must be at least 2.
integer3This parameter is used by GATK variant filteration step. It defines the number of SNPs which make up a cluster within a window. Must be at least 2.
Value to be used for the FisherStrand (FS) filter
number30This parameter defines the value to use for the FisherStrand (FS) filter in the GATK variant-filtering step.
The value should given in a float number format. Default is 30.0
Value to be used for the QualByDepth (QD) filter
number2This parameter defines the value to use for the QualByDepth (QD) filter in the GATK variant-filtering step.
The value should given in a float number format. Default is 2.0
Parameters 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/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional 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.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom 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
booleantrueShow all params when using --help
booleanBy default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.
Validation of parameters fails when an unrecognised parameter is found.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.
Base URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/dataBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data