Identify chromosomal rearrangements.
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
input:file
BAM/CRAM file
*.{bam,cram}
input_index:file
BAM/CRAM index file
*.{bai,crai}
meta2:map
Groovy Map containing sample information e.g. [ id:'test_fasta']
[ id:'test_fasta']
fasta:file
Input FASTA file
*.{fasta,fa}
meta3:map
Groovy Map containing sample information from bwa index e.g. [ id:'test_bwa-index' ]
[ id:'test_bwa-index' ]
bwa_index:file
BWA genome index files
Directory containing BWA index *.{amb,ann,bwt,pac,sa}
vcf
*.vcf:file
*.{vcf}
ploidy
*.ploidies.tab:file
tab
*.{ploidies.tab}
versions
versions.yml:file
File containing software versions
versions.yml
Search for structural variants.
