nf-core/pacsomatic
Nextflow pipeline for PacBio HiFi tumor/normal somatic genomics
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.
stringReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Do not load the iGenomes reference config.
booleanThe base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Options for variant calling specifications
Name of a prepackaged Clair3 model.
stringDirectory containing Clair3 model files.
stringminmapq value for pbcpgtools
number1min-coverage value for pbcpgtools
number4Genome assembly name for VEP annotation, e.g., GRCh38 or GRCh37.
stringSpecies name for VEP annotation, e.g., homo_sapiens or mus_musculus.
stringSpecify the version of the VEP cache provided to the --vep_cache option.
integer115Directory for Ensembl VEP Cache.
stringmutationalpattern max_delta
number0.06Parameters for structural variant (SV) calling, filtering, and annotation
Tandem repeat regions BED file for SEVERUS
string^\S+\.bed$Control VCF file for SVPACK filtering
string^\S+\.vcf(\.gz)?$Reference GFF file for SVPACK annotation
string^\S+\.gff3?(\.gz)?$AnnotSV cache directory
stringOptions for copy number variation (CNV) calling and analysis
BED file defining target regions for CNVkit analysis
stringCNVkit reference file for copy number calling
stringGermline VCF file for CNV refinement
stringAverage target region size for CNVkit
integerMinimum variant depth for CNVkit analysis
integer20Parameters for tumor clonality analysis using Hartwig Medical Foundation tools (AMBER, COBALT, PURPLE)
GermlineHetPon VCF file for AMBER
string^\S+\.vcf(\.gz)?$GC content profile for COBALT
string^\S+\.(cnp|txt)$Driver gene panel for PURPLE
string^\S+\.(tsv|txt|bed)$Known somatic hotspot variants for PURPLE
string^\S+\.vcf(\.gz)?$Known germline hotspot variants for PURPLE
string^\S+\.vcf(\.gz)?$Ensembl data directory for PURPLE
stringTarget regions BED file for targeted sequencing
string^\S+\.bed$Diploid regions BED file for copy number baseline
string^\S+\.bed$Target region normalisation file for COBALT
string^\S+\.(tsv|txt)$Options to skip various steps within the workflow.
Skip all QC.
booleanSkip Mosdepth.
booleanSkip Bamcoverage.
booleanOption to skip deepsomatic SNV_INDEL caller
booleanOption to skip Ensembl VEP for somatic SNV annotation
booleanOption to skip VEP cache download (use existing —vep_cache instead)
booleanOption to skip germline hiphase for all samples
booleanOption to skip pb_cpg_tools
booleanOption to skip DSS for differential methylation region detection
booleanOption to skip dmr annotation
booleanOption to skip somatic hiphase
booleanOption to skip mutationalpattern
booleanOption to skip tumor_clonality
booleanOption to skip SV caller
booleanOption to skip svpack for SV filtering and annotation
booleanOption to skip annotsv
booleanOption to skip AnnotSV annotation database installation (use existing —annotsv_cache instead)
booleanOption to skip CNVKit caller
booleanOption to skip HRD(Homologous Recombination Deficiency) estimation from the called SNV and SV variants
booleanSkip MultiQC.
booleanOptions for specifying workflow type
Workflow type - can either be wes or wgs
stringParameters 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/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string