Align reads to a reference genome using bowtie2 then sort with samtools
meta :map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
ch_reads :file
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
ch_index :file
Bowtie2 genome index files
*.ebwt
save_unaligned :boolean
Save reads that do not map to the reference (true) or discard them (false) (default: false)
sort_bam :boolean
Use samtools sort (true) or samtools view (false)
ch_fasta :file
Reference fasta file
*.{fasta,fa}
bam :file
Output BAM file containing read alignments
*.{bam}
versions :file
File containing software versions
versions.yml
fastq :file
Unaligned FastQ files
*.fastq.gz
log :file
Alignment log
*.log
