nf-core/rnavar

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 tab or comma-separated file with a header row or a JSON/YAML file. See usage docs.

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.

If 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.

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.

NB If none provided, will be generated automatically from the FASTA reference.

NB If none provided, will be generated automatically from the FASTA reference

This parameter is mandatory if --genome is not specified.

This parameter must be specified if --genome or --gtf are not specified.

Specify the read length for the STAR aligner.

If 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.

If 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.

If 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.

If you use AWS iGenomes, this has already been set for you appropriately. Alternatively species listed in Ensembl Genomes caches can be used.

If 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

Set this parameter, if you wish to download annotation cache.

Specify true for removing duplicates from BAM file during Picard MarkDuplicates step.

This parameter define which aligner is to be used for aligning the RNA reads to the reference genome.

This 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.

This parameter enables STAR to perform 2-pass mapping. Default true.

Do not use parameter --sjdbGTFfile <GTF file> during the STAR genomeGenerate process.

This parameter specifies the maximum available RAM (bytes) for sorting BAM during STAR alignment.

This parameter specifies the number of bins to be used for coordinate sorting during STAR alignment step.

This parameter is required for creating a proper BAM header to use in the downstream analysis of GATK.

This parameter is required for creating a proper BAM header to use in the downstream analysis of GATK.

This may either be in the form of FastQ or BAM files depending on the options available for that particular tool.

By 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.

More details can be found in the UMI-tools documentation.

More details can be found in the UMI-tools documentation.

Specify the minimum phred-scaled confidence threshold at which variants should be called.

This parameter enables GATK HAPLOTYPECALLER to generate GVCFs. Default false.

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 which should contain the relevant genome and build directory in the path ${snpeff_species}.${snpeff_version}

For details, see here.

To 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/

To be used with --vep_dbnsfp.

To 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'.

To 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.

For details, see here.

For details, see here.

To be used with --vep_spliceai.

To be used with --vep_spliceai.

To be used with --vep_spliceai.

To be used with --vep_spliceai.

For details, see here and here.

Using this parameter, you can add custom args to VEP.

This parameter disable the base recalibration step, thus using a un-calibrated BAM file for variant calling.

This 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.

Set this parameter if you don't want to filter any variants.

Set this parameter if you don't want to run variant annotation.

This parameter disable all QC reports

Set this parameter if you don't want to the pipeline to check and filter unknown regions in the exon bed file.

Set this parameter to decide the number of splits for the gene interval list file.

This 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

This 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'.

This 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.

This 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.

This 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.