nf-core/sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
2.7.1). The latest
stable release is
3.5.1
.
Define where the pipeline should find input data and save output data.
Path to input file(s).
stringStarting step.
stringThe output directory where the results will be saved.
string./resultsOption used for most of the pipeline
Tools to use for variant calling and/or for annotation.
stringnullDisable usage of intervals.
booleanEstimate interval size.
number1000Enable Sentieon if available.
booleanDisable specified QC and Reporting tools.
stringnullTarget BED file for whole exome or targeted sequencing.
stringRun Trim Galore.
booleanRemove bp from the 5’ end of read 1.
integerRemove bp from the 5’ end of read 2.
integerRemove bp from the 3’ end of read 1 AFTER adapter/quality trimming has been performed.
integerRemove bp from the 3’ end of read 2 AFTER adapter/quality trimming has been performed.
integerApply the —nextseq=X option, to trim based on quality after removing poly-G tails.
integerSave trimmed FastQ file intermediates
booleanSpecify how many reads should be contained in the split FastQ file
numberSpecify aligner to be used to map reads to reference genome.
stringEstablish values for GATK MarkDuplicates memory consumption
string-Xms4000m -Xmx7gEnable usage of GATK Spark implementation
booleanSave Mapped BAMs
booleanSkip GATK MarkDuplicates
booleanOverwrite ASCAT ploidy
stringnullOverwrite ASCAT purity
stringnullOverwrite Control-FREEC coefficientOfVariation
number0.05Overwrite Control-FREEC contaminationAdjustement
booleanDesign known contamination value for Control-FREEC
stringnullOverwrite Control-FREEC ploidy
number2Overwrite Control-FREEC window size
numberGenerate g.vcf output from GATK HaplotypeCaller
booleanWill not use Manta candidateSmallIndels for Strelka
booleanPanel-of-normals VCF (bgzipped) for GATK Mutect2 / Sentieon TNscope
stringIndex of PON panel-of-normals VCF
stringDo not analyze soft clipped bases in the reads for GATK Mutect2
booleanIf provided, UMIs steps will be run to extract and annotate the reads with UMI and create consensus reads
booleanWhen processing UMIs, a read structure should always be provided for each of the fastq files.
stringnullWhen processing UMIs, a read structure should always be provided for each of the fastq files.
stringnullSpecify from which tools Sarek should look for VCF files to annotate
stringnullEnable the use of cache for annotation
booleanEnable CADD cache.
booleanPath to CADD InDels file.
stringnullPath to CADD InDels index.
stringnullPath to CADD SNVs file.
stringnullPath to CADD SNVs index.
stringnullEnable the use of the VEP GeneSplicer plugin.
booleanPath to snpEff cache
stringnullPath to VEP cache
stringnullOptions for the reference genome files
Name of iGenomes reference.
stringPath to ASCAT loci file.
stringPath to ASCAT GC correction file.
stringPath to BWA mem indices.
stringPath to chromosomes folder.
stringPath to chromosomes length file.
stringPath to dbsnp file.
stringPath to dbsnp index.
stringPath to FASTA dictionary file.
stringPath to FASTA genome file.
stringPath to FASTA reference index.
stringPath to GATK Mutect2 Germline Resource File
stringPath to GATK Mutect2 Germline Resource Index
stringPath to intervals file
stringPath to known indels file
stringPath to known indels file index
stringPath to Control-FREEC mappability file
stringsnpEff DB version
stringsnpEff species
stringVEP cache version
stringSave built references
booleanDirectory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDirectory / URL base for genomes references.
stringnullDo not load the iGenomes reference config.
booleanLess 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.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Boolean whether to validate parameters against the schema at runtime
booleantrueEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MBDo not use coloured log outputs.
booleanPath to MultiQC custom config file.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoName of sequencing center to be displayed in BAM file
stringnullShow all params when using --help
booleanSet the top limit for requested resources for any single job.
integer8Use to set memory for a single CPU.
string7 GBMaximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$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/masterInstitutional configs hostname.
stringInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
string