Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
input_1{:bash}
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
input_1_index{:bash}
:file
BAM/CRAM/SAM index file
*.{bai,crai}
input_2{:bash}
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
input_2_index{:bash}
:file
BAM/CRAM/SAM index file
*.{bai,crai}
target_bed{:bash}
:file
Optional - Limit analysis to targets listed in this BED-format FILE.
*.bed
meta2{:bash}
:map
Groovy Map containing reference information.
e.g. [ id:‘test_reference’ ]
fasta{:bash}
:file
reference fasta file
.{fa,fa.gz,fasta,fasta.gz}
meta3{:bash}
:map
Groovy Map containing reference information.
e.g. [ id:‘test_reference’ ]
fasta_fai{:bash}
:file
reference fasta file index
*.{fa,fasta}.fai
meta4{:bash}
:map
Groovy Map containing meta information for the samples file.
e.g. [ id:‘test_samples’ ]
samples{:bash}
:file
Optional - Limit analysis to samples listed (one per line) in the FILE.
*.txt
meta5{:bash}
:map
Groovy Map containing meta information for the populations file.
e.g. [ id:‘test_populations’ ]
populations{:bash}
:file
Optional - Each line of FILE should list a sample and a population which it is part of.
*.txt
meta6{:bash}
:map
Groovy Map containing meta information for the cnv file.
e.g. [ id:‘test_cnv’ ]
cnv{:bash}
:file
A copy number map BED file, which has either a sample-level ploidy:
sample_name copy_number
or a region-specific format:
seq_name start end sample_name copy_number
*.bed
Output
name:type
description
pattern
vcf{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.vcf.gz{:bash}
:file
Compressed VCF file
*.vcf.gz
versions{:bash}
versions.yml{:bash}
:file
File containing software version
versions.yml
Tools
freebayes
MIT
Bayesian haplotype-based polymorphism discovery and genotyping
