nf-core/pgdb
The ProteoGenomics database generation workflow creates different protein databases for ProteoGenomics data analysis.
22.10.6.
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Add ENSEMBL canonical proteomes
Add the reference proteome to the file
booleantruePath to configuration file for ENSEMBL download parameters
stringPath to configuration file for parameters in generating protein databases from ENSMEBL sequences
stringURL for downloading GENCODE datafiles
stringftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19Taxonomic term for the species to download from ENSEMBL
stringhomo_sapiensNon canonical proteins generation parameters
Generate protein database from non-coding RNA
booleanGenerate protein database from pseudogenes
booleanGenerate alternative ORFs from canonical proteins
booleanDownload ENSEMBL variants and generate protein database
booleanProteins generated using an input VCF
Enable translation of a given VCF file
booleanVCF file path to be translated. Generate variants proteins by modifying sequences of affected transcripts.
stringAllele frequency identifier string in VCF Info column, if no AF info is given set it to empty.
stringcBioportal variant parameters
Download cBioPortal studies and generate protein database
booleanSpecify a tissue type to limit the cBioPortal mutations to a particular caner type
stringallSpecify a column from the clinical sample file to be used for filtering records
stringCANCER_TYPEDownload mutations from a specific study in cbiportal default is all which downloads mutations from all studies
stringcBioPortal configuration file
stringCOSMIC variant proteins parameters
Download COSMIC mutation files and generate protein database
booleanDownload COSMIC cell line files and generate protein database
stringUser name (or email) for COSMIC account
stringPassword for COSMIC account
stringPath to configuration file for parameters in generating
stringSpecify a tissue type to limit the COSMIC mutations to a particular caner type
stringallSpecify a sample name to limit the COSMIC cell line mutations to a particular cell line
stringallAdd gNOMAD variants to the database
booleangNOMAD url
stringgs://gnomad-public/release/2.1.1/vcf/exomes/gnomad.exomes.r2.1.1.sites.vcf.bgzGenerate decoy proteins and attach them to the final protein database
Append the decoy proteins to the database
booleanString to be used as prefix for the generated decoy sequences
stringDecoy_Method used to generate the decoy database
stringEnzyme used to generate the decoy
stringTrypsinConfiguration file to perform the decoy generation
stringClean and process the resulted database
Clean the database for stop codons, short protein sequences
booleanMinimum number of AminoAcids for a protein to be included in the database
integer6If an stop codons is found, create two proteins from it
booleanDefine where the pipeline should find input data and save output data.
The output directory where the results will be saved.
string./resultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Filename for the final protein database
stringfinal_proteinDB.faLess common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MBDo not use coloured log outputs.
booleanDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoShow all params when using --help
booleanSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^[\d\.]+\s*.(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+(\.\d+)?(?:\s*|\.?)(s|m|h|d)\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