nf-core/sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
2.7.1
). The latest
stable release is
3.5.1
.
Define where the pipeline should find input data and save output data.
Path to input file(s).
string
Starting step.
string
The output directory where the results will be saved.
string
./results
Option used for most of the pipeline
Tools to use for variant calling and/or for annotation.
string
null
Disable usage of intervals.
boolean
Estimate interval size.
number
1000
Enable Sentieon if available.
boolean
Disable specified QC and Reporting tools.
string
null
Target BED file for whole exome or targeted sequencing.
string
Run Trim Galore.
boolean
Remove bp from the 5’ end of read 1.
integer
Remove bp from the 5’ end of read 2.
integer
Remove bp from the 3’ end of read 1 AFTER adapter/quality trimming has been performed.
integer
Remove bp from the 3’ end of read 2 AFTER adapter/quality trimming has been performed.
integer
Apply the —nextseq=X option, to trim based on quality after removing poly-G tails.
integer
Save trimmed FastQ file intermediates
boolean
Specify how many reads should be contained in the split FastQ file
number
Specify aligner to be used to map reads to reference genome.
string
Establish values for GATK MarkDuplicates memory consumption
string
-Xms4000m -Xmx7g
Enable usage of GATK Spark implementation
boolean
Save Mapped BAMs
boolean
Skip GATK MarkDuplicates
boolean
Overwrite ASCAT ploidy
string
null
Overwrite ASCAT purity
string
null
Overwrite Control-FREEC coefficientOfVariation
number
0.05
Overwrite Control-FREEC contaminationAdjustement
boolean
Design known contamination value for Control-FREEC
string
null
Overwrite Control-FREEC ploidy
number
2
Overwrite Control-FREEC window size
number
Generate g.vcf output from GATK HaplotypeCaller
boolean
Will not use Manta candidateSmallIndels for Strelka
boolean
Panel-of-normals VCF (bgzipped) for GATK Mutect2 / Sentieon TNscope
string
Index of PON panel-of-normals VCF
string
Do not analyze soft clipped bases in the reads for GATK Mutect2
boolean
If provided, UMIs steps will be run to extract and annotate the reads with UMI and create consensus reads
boolean
When processing UMIs, a read structure should always be provided for each of the fastq files.
string
null
When processing UMIs, a read structure should always be provided for each of the fastq files.
string
null
Specify from which tools Sarek should look for VCF files to annotate
string
null
Enable the use of cache for annotation
boolean
Enable CADD cache.
boolean
Path to CADD InDels file.
string
null
Path to CADD InDels index.
string
null
Path to CADD SNVs file.
string
null
Path to CADD SNVs index.
string
null
Enable the use of the VEP GeneSplicer plugin.
boolean
Path to snpEff cache
string
null
Path to VEP cache
string
null
Options for the reference genome files
Name of iGenomes reference.
string
Path to ASCAT loci file.
string
Path to ASCAT GC correction file.
string
Path to BWA mem indices.
string
Path to chromosomes folder.
string
Path to chromosomes length file.
string
Path to dbsnp file.
string
Path to dbsnp index.
string
Path to FASTA dictionary file.
string
Path to FASTA genome file.
string
Path to FASTA reference index.
string
Path to GATK Mutect2 Germline Resource File
string
Path to GATK Mutect2 Germline Resource Index
string
Path to intervals file
string
Path to known indels file
string
Path to known indels file index
string
Path to Control-FREEC mappability file
string
snpEff DB version
string
snpEff species
string
VEP cache version
string
Save built references
boolean
Directory / URL base for iGenomes references.
string
s3://ngi-igenomes/igenomes
Directory / URL base for genomes references.
string
null
Do not load the iGenomes reference config.
boolean
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
Email address for completion summary.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
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
Path to MultiQC custom config file.
string
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
Name of sequencing center to be displayed in BAM file
string
null
Show all params when using --help
boolean
Set the top limit for requested resources for any single job.
integer
8
Use to set memory for a single CPU.
string
7 GB
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.h
^(\d+\.?\s*(s|m|h|day)\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