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