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})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
Filename for the final protein database
stringfinal_proteinDB.faLess common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Boolean whether to validate parameters against the schema at runtime
booleantrueEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$This works exactly as with --email, except emails are only sent if the workflow is not successful.
Send plain-text email instead of HTML.
booleanSet to receive plain-text e-mails instead of HTML formatted.
File size limit when attaching MultiQC reports to summary emails.
string25.MBIf file generated by pipeline exceeds the threshold, it will not be attached.
Do not use coloured log outputs.
booleanSet to disable colourful command line output and live life in monochrome.
Directory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoShow all params when using --help
booleanSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^[\d\.]+\s*.(K|M|G|T)?B$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+(\.\d+)?(?:\s*|\.?)(s|m|h|d)\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'
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterProvide git commit id for custom Institutional configs hosted at nf-core/configs. This was implemented for reproducibility purposes. Default: master.
## Download and use config file with following git commit id
--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96
Base 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 the custom_config_base option. For example:
## Download and unzip the config files
cd /path/to/my/configs
wget https://github.com/nf-core/configs/archive/master.zip
unzip master.zip
## Run the pipeline
cd /path/to/my/data
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/
Note that the nf-core/tools helper package has a
downloadcommand to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.
Institutional configs hostname.
stringInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
string