Maps the reads to the reference database
meta
:map
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
fasta
:file
fastq file with reads
*.{.fastq,.fq,.fastq.gz,fq.gz}
meta2
Groovy Map containing index genome id and path e.g. [ id:‘test’, ‘bowtie2’ ]
index
Directory with Bowtie2 genome index files
*.ebwt
bam
*.bam
Alignment (BAM) file of reads mapped to the reference database
*.{bam}
versions_coptr
${task.process}
:string
The name of the process
coptr
The name of the tool
coptr |& sed -E '11!d ; s/CoPTR.*?\(v(.*?)\).*/\1/'
:eval
The expression to obtain the version of the tool
versions
Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.
