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