structural-variant calling with sniffles
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’ ]
input
:file
A single .bam/.cram file - OR - one or more .snf files - OR - a single .tsv file containing a list of .snf files and optional sample ids as input
*.{bam,cram,snf,tsv}
index
Index of BAM/CAM file
*.{bai,crai}
meta2
Groovy Map containing reference information e.g. [ id:‘fasta’ ]
fasta
Reference database in FASTA format
meta3
Groovy Map containing tandem repeat information e.g. [ id:‘hg38’ ]
tandem_file
Tandem repeat file
*.bed
vcf_output
VCF output file
*.vcf.gz
snf_output
SNF output file
vcf
Compressed VCF file
tbi
*.vcf.gz.tbi
Compressed VCF file index
*.tbi
snf
*.snf
SNF file
versions_sniffles
${task.process}
:string
The name of the process
sniffles
The name of the tool
sniffles --version | sed 's/.* //g'
:eval
The expression to obtain the version of the tool
versions
a fast structural variant caller for long-read sequencing
