Generate a consensus sequence from a BAM file using iVar
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam
:file
A sorted (with samtools sort) and trimmed (with iVar trim) bam file
*.bam
fasta
The reference sequence used for mapping and generating the BAM file
*.fa
save_mpileup
:boolean
Save mpileup file generated by ivar consensus
*.mpileup
iVar generated consensus sequence
qual
*.qual.txt
iVar generated quality file
mpileup
mpileup output from samtools mpileup [OPTIONAL]
versions_ivar
${task.process}
:string
The name of the process
ivar
The name of the tool
ivar version | sed -n 's|iVar version \(.*\)|\1|p'
:eval
The expression to obtain the version of the tool
versions
iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
