Identify chromosomal rearrangements.
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input
:file
BAM/CRAM file
*.{bam,cram}
input_index
BAM/CRAM index file
*.{bai,crai}
meta2
Groovy Map containing sample information e.g. [ id:'test_fasta']
[ id:'test_fasta']
fasta
Input FASTA file
*.{fasta,fa}
fai
Input FASTA index file
*.{fai}
meta3
Groovy Map containing sample information from bwa index e.g. [ id:'test_bwa-index' ]
[ id:'test_bwa-index' ]
bwa_index
BWA genome index files
Directory containing BWA index *.{amb,ann,bwt,pac,sa}
vcf
${prefix}.vcf
*.{vcf}
ploidy
${prefix}.ploidies.tab
tab
*.{ploidies.tab}
versions_tiddit
${task.process}
:string
The name of the process
tiddit
The name of the tool
tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'
:eval
The expression to obtain the version of the tool
versions
Search for structural variants.
