Determines the gender of a sample from the BAM/CRAM file.
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
One or more BAM/CRAM files to determine the gender of
*.{bam,cram}
bai{:bash}
The index file(s) from the input BAM/CRAM file(s)
*.{bai,crai}
meta2{:bash}
Groovy Map containing reference fasta information e.g. [ id:‘test’ ]
fasta{:bash}
The reference FASTA to use (mandatory when CRAM files are used)
*.{fasta,fa,fna}
meta3{:bash}
fai{:bash}
The index file from the reference FASTA
*.fai
method{:bash}
:string
The method to use to define the gender (possibilities are ‘xy’, ‘hetx’ and ‘sry’)
(xy|hetx|sry)
tsv{:bash}
*.tsv{:bash}
An output TSV file containing the results of the gender prediction
*.tsv
versions_ngsbits{:bash}
${task.process}{:bash}
The name of the process
ngsbits{:bash}
The name of the tool
SampleGender --version 2>&1 | sed 's/SampleGender //'{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
Short-read sequencing tools
