Calling lowest common ancestors from multi-mapped reads in SAM/BAM/CRAM files
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
bai
BAM/CRAM/SAM index
*.{bai,.crai}
database
Directory containing the sam2lca database
*
csv
*.csv
CSV file containing the sam2lca results
json
*.json
JSON file containing the sam2lca results
*.bam
Optional sorted BAM/CRAM/SAM file annotated with LCA taxonomic information
versions_sam2lca
${task.process}
:string
The name of the process
sam2lca
The name of the tool
sam2lca --version | sed 's/.*version //'
:eval
The expression to obtain the version of the tool
versions
Lowest Common Ancestor on SAM/BAM/CRAM alignment files
