Description

Checks that all data in the set of input files appear to come from the same individual

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

input1 (file)

List containing 1 or more bam/vcf files or a file containing filepaths

*.{bam,vcf,vcf.gz,txt,fofn}

input1_index (file)

List containing 1 or more bam/vcf files indexes

*.{bai,csi,crai,tbi}

input2 (file)

Optional list containing 1 or more bam/vcf files or a file containing filepaths

*.{bam,vcf,vcf.gz,txt,fofn}

input2_index (file)

List containing 1 or more bam/vcf files indexes

*.{bai,csi,crai,tbi}

haplotype_map (file)

Haplotype map file

*.{txt,vcf,vcf.gz}

meta2 (map)

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

fasta (file)

Reference genome file

*.{fasta,fa,fasta.gz,fa.gz}

fasta_index (file)

Reference genome index file

*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

crosscheck_metrics (file)

Metrics created by crosscheckfingerprints

*.{crosscheck_metrics.txt}

versions (file)

File containing software versions

versions.yml

Tools

picard
MIT

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.