nf-core/hlatyping
Precision HLA typing from next-generation sequencing data
1.2.0). The latest
stable release is
2.1.0
.
Define where the pipeline should find input data and save output data.
Input FastQ or BAM files.
stringInput multiple FastQ or BAM files.
stringundefinedSpecifies that the input is single-end reads.
booleanSpecifies that the input is in BAM format.
booleanSpecifies whether the input is DNA or RNA.
stringdnaThe 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})$Options for the optimisation step of the HLA typing pipeline.
Specifies the integer programming solver.
stringglpkSpecifies the number of output solutions.
integer1Specifies the weight of the regularisation term.
number0.009Options for the reference genome indices used to align reads.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/Do not load the iGenomes reference config.
booleanPath for the mapping reference index location.
string$baseDir/data/indices/yaraName of the mapping reference index.
stringLess common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringWorkflow name.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MBDo not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoSet 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.GBMaximum amount of time that can be requested for any single job.
string240.hParameters 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 description.
stringInstitutional config contact information.
stringInstitutional config URL link.
string