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.
string
Input multiple FastQ or BAM files.
string
undefined
Specifies that the input is single-end reads.
boolean
Specifies that the input is in BAM format.
boolean
Specifies whether the input is DNA or RNA.
string
dna
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})$
Options for the optimisation step of the HLA typing pipeline.
Specifies the integer programming solver.
string
glpk
Specifies the number of output solutions.
integer
1
Specifies the weight of the regularisation term.
number
0.009
Options for the reference genome indices used to align reads.
Directory / URL base for iGenomes references.
string
s3://ngi-igenomes/igenomes/
Do not load the iGenomes reference config.
boolean
Path for the mapping reference index location.
string
$baseDir/data/indices/yara
Name of the mapping reference index.
string
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
Method used to save pipeline results to output directory.
string
Workflow name.
string
Email address for completion summary, only when pipeline fails.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
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
Custom config file to supply to MultiQC.
string
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
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
Maximum amount of time that can be requested for any single job.
string
240.h
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 description.
string
Institutional config contact information.
string
Institutional config URL link.
string