Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
input_1
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
input_1_index
:file
BAM/CRAM/SAM index file
*.{bai,crai}
input_2
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
input_2_index
:file
BAM/CRAM/SAM index file
*.{bai,crai}
target_bed
:file
Optional - Limit analysis to targets listed in this BED-format FILE.
*.bed
meta2
:map
Groovy Map containing reference information.
e.g. [ id:‘test_reference’ ]
fasta
:file
reference fasta file
.{fa,fa.gz,fasta,fasta.gz}
meta3
:map
Groovy Map containing reference information.
e.g. [ id:‘test_reference’ ]
fasta_fai
:file
reference fasta file index
*.{fa,fasta}.fai
meta4
:map
Groovy Map containing meta information for the samples file.
e.g. [ id:‘test_samples’ ]
samples
:file
Optional - Limit analysis to samples listed (one per line) in the FILE.
*.txt
meta5
:map
Groovy Map containing meta information for the populations file.
e.g. [ id:‘test_populations’ ]
populations
:file
Optional - Each line of FILE should list a sample and a population which it is part of.
*.txt
meta6
:map
Groovy Map containing meta information for the cnv file.
e.g. [ id:‘test_cnv’ ]
cnv
: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
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.vcf.gz
:file
Compressed VCF file
*.vcf.gz
versions_freebayes
${task.process}
:string
The name of the process
freebayes
:string
The name of the tool
freebayes --version 2>&1 | sed "s/version:\s*v//g"
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
freebayes
:string
The name of the tool
freebayes --version 2>&1 | sed "s/version:\s*v//g"
:eval
The expression to obtain the version of the tool
Tools
freebayes
MIT
Bayesian haplotype-based polymorphism discovery and genotyping
