Determines the gender of a sample from the BAM/CRAM file.
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bam:file
One or more BAM/CRAM files to determine the gender of
*.{bam,cram}
bai:file
The index file(s) from the input BAM/CRAM file(s)
*.{bai,crai}
meta2:map
Groovy Map containing reference fasta information e.g. [ id:‘test’ ]
fasta:file
The reference FASTA to use (mandatory when CRAM files are used)
*.{fasta,fa,fna}
fai:file
The index file from the reference FASTA
*.fai
method:string
The method to use to define the gender (posibilities are ‘xy’, ‘hetx’ and ‘sry’)
(xy|hetx|sry)
tsv
*.tsv:file
An output TSV file containing the results of the gender prediction
*.tsv
versions
versions.yml:file
File containing software versions
versions.yml
Short-read sequencing tools
