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
boolean
true
Path to configuration file for ENSEMBL download parameters
string
Path to configuration file for parameters in generating protein databases from ENSMEBL sequences
string
URL for downloading GENCODE datafiles
string
ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19
Taxonomic term for the species to download from ENSEMBL
string
homo_sapiens
Non canonical proteins generation parameters
Generate protein database from non-coding RNA
boolean
Generate protein database from pseudogenes
boolean
Generate alternative ORFs from canonical proteins
boolean
Download ENSEMBL variants and generate protein database
boolean
Proteins generated using an input VCF
Enable translation of a given VCF file
boolean
VCF file path to be translated. Generate variants proteins by modifying sequences of affected transcripts.
string
Allele frequency identifier string in VCF Info column, if no AF info is given set it to empty.
string
cBioportal variant parameters
Download cBioPortal studies and generate protein database
boolean
Specify a tissue type to limit the cBioPortal mutations to a particular caner type
string
all
Specify a column from the clinical sample file to be used for filtering records
string
CANCER_TYPE
Download mutations from a specific study in cbiportal default is all which downloads mutations from all studies
string
cBioPortal configuration file
string
COSMIC variant proteins parameters
Download COSMIC mutation files and generate protein database
boolean
Download COSMIC cell line files and generate protein database
string
User name (or email) for COSMIC account
string
Password for COSMIC account
string
Path to configuration file for parameters in generating
string
Specify a tissue type to limit the COSMIC mutations to a particular caner type
string
all
Specify a sample name to limit the COSMIC cell line mutations to a particular cell line
string
all
Add gNOMAD variants to the database
boolean
gNOMAD url
string
gs://gnomad-public/release/2.1.1/vcf/exomes/gnomad.exomes.r2.1.1.sites.vcf.bgz
Generate decoy proteins and attach them to the final protein database
Append the decoy proteins to the database
boolean
String to be used as prefix for the generated decoy sequences
string
Decoy_
Method used to generate the decoy database
string
Enzyme used to generate the decoy
string
Trypsin
Configuration file to perform the decoy generation
string
Clean and process the resulted database
Clean the database for stop codons, short protein sequences
boolean
Minimum number of AminoAcids for a protein to be included in the database
integer
6
If an stop codons is found, create two proteins from it
boolean
Define where the pipeline should find input data and save output data.
The output directory where the results will be saved.
string
./results
Email address for completion summary.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
Filename for the final protein database
string
final_proteinDB.fa
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
Method used to save pipeline results to output directory.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Email 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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
Do not use coloured log outputs.
boolean
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
Show all params when using --help
boolean
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
^[\d\.]+\s*.(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.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.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional configs hostname.
string
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string