nf-core/rnavar
gatk4 RNA variant calling pipeline
1.0.0
). The latest
stable release is
1.1.0
.
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
string
^\S+\.csv$
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Email address for completion summary.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
string
Save FastQ files after merging re-sequenced libraries in the results directory.
boolean
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
Path to FASTA genome file.
string
^\S+\.fn?a(sta)?(\.gz)?$
Path to FASTA dictionary file.
string
Path to FASTA reference index.
string
Directory / URL base for iGenomes references.
string
s3://ngi-igenomes/igenomes
Do not load the iGenomes reference config.
boolean
Path to GTF annotation file.
string
Path to GFF3 annotation file.
string
Path to BED file containing exon intervals. This will be created from the GTF file if not specified.
string
Read length
number
151
If generated by the pipeline, save the STAR index in the results directory.
boolean
Path to known indels VCF file
string
Path to known indels index file
string
Path to dbSNP VCF file
string
Path to dbSNP VCF index file
string
snpEff DB version
string
VEP genome
string
VEP species
string
VEP cache version
string
Define parameters related to read alignment
Specifies the alignment algorithm to use. Currently available option is ‘star’
string
star
Path to STAR index folder or compressed file (tar.gz)
string
Enable STAR 2-pass mapping mode.
boolean
Do not use GTF file during STAR index buidling step
boolean
Option to limit RAM when sorting BAM file. Value to be specified in bytes. If 0, will be set to the genome index size.
integer
Specifies the number of genome bins for coordinate-sorting
integer
50
Specifies the maximum number of collapsed junctions
integer
1000000
Sequencing center information to be added to read group of BAM files.
string
Specify the sequencing platform used
string
illumina
Where possible, save unaligned reads from aligner to the results directory.
boolean
Save the intermediate BAM files from the alignment step.
boolean
Create a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes.
boolean
Specify whether to remove duplicates from the BAM during Picard MarkDuplicates step.
boolean
The minimum phred-scaled confidence threshold at which variants should be called.
number
20
Specify which tools RNAvar should use for annotating variants. Values can be ‘snpeff’, ‘vep’ or ‘merge’. If you specify ‘merge’, the pipeline runs both snpeff and VEP annotation.
string
Enable the use of cache for annotation
boolean
Enable CADD cache.
boolean
Path to CADD InDels file.
string
Path to CADD InDels index.
string
Path to CADD SNVs file.
string
Path to CADD SNVs index.
string
Enable the use of the VEP GeneSplicer plugin.
boolean
Path to snpEff cache
string
Path to VEP cache
string
Define parameters that control the stages in the pipeline
Skip the process of base recalibration steps i.e., GATK BaseRecalibrator and GATK ApplyBQSR.
boolean
Skip the process of preparing interval lists for the GATK variant calling step
boolean
Skip variant filtering of GATK
boolean
Skip variant annotation
boolean
Skip MultiQC reports
boolean
Define parameters of the tools used in the pipeline
Number of times the gene interval list to be split in order to run GATK haplotype caller in parallel
integer
25
Do not use gene interval file during variant calling
boolean
The window size (in bases) in which to evaluate clustered SNPs.
integer
35
The number of SNPs which make up a cluster. Must be at least 2.
integer
3
Value to be used for the FisherStrand (FS) filter
number
30
Value to be used for the QualByDepth (QD) filter
number
2
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 config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
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+(\.\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*)+$
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, 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
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
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
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean
Run this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
boolean