Computes the depth at each position or region.
meta1{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
sorted BAM/CRAM/SAM file
*.{bam,cram,sam}
index{:bash}
BAM/CRAM index file
*.{bai,crai}
meta2{:bash}
Groovy Map containing sample information e.g. [ id:‘test’ ]
intervals{:bash}
list of positions or regions in specified bed file
*.{bed}
tsv{:bash}
*.tsv{:bash}
The output of samtools depth has three columns - the name of the contig or chromosome, the position and the number of reads aligned at that position
*.{tsv}
versions_samtools{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
samtools{:bash}
The tool name
samtools version | sed "1!d;s/.* //"{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
Tools for dealing with SAM, BAM and CRAM files; samtools depth – computes the read depth at each position or region
